AFNI HISTORY
all levels
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -type BUG_FIX
---- log of AFNI updates (most recent first) ----
10 Oct 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
mask intersect inputs did not have views
Thanks to martinsingua on the MB for pointing out the problem.
24 Sep 2024, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 4 (BUG_FIX)
fix confusion over auto-gzip BRIK name
23 Jul 2024, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
undo the the problematic -f change from 2024/04/26
The -f was added to tcsh to prevent biowulf from updating the PATH
when using whereami, as they have a different program with that name.
But -f means that on macs DYLD vars would not be set, crashing afni
when using the macos_10.12_local binaries.
30 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix volreg TSNR for ME: use eind -> fave_echo
Thanks to zhengchencai on MB for pointing out the problem.
07 May 2024, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
3dCM briefly required a mask
Thanks to P Kundu for pointing out the problem.
22 Apr 2024, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
singleton coordinates should round to the closest voxel center
Originally, box coordinates rounded to the nearest voxel, effectively
extending ranges by 1/2 voxel on each side. This was changed in 2021 to
be strict. But then singleton coordinates often hit no voxels, and the
help says one voxel should be found.
Now a singleton coordinate will round to the nearest center, while a ':'
separated range will be precise, as with the mixed use:
-xbox 5.4:11.3 -17.8:-4.1 11
Here, the '11' will be rounded to the closest center.
17 Apr 2024, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
in THD_load_nifti(), need_copy might imply scale_data
Thanks to @liningpan on github for reporting this.
12 Mar 2024, RC Reynolds, SUMA, level 2 (MINOR), type 4 (BUG_FIX)
updates to SUMA_CreateDO.c, SUMA_Color.c, SUMA_driver.c
Some build machines need to adhere to the C99 standard.
07 Mar 2024, RC Reynolds, abids_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
use compare_py_ver_to_given() for comparison of python versions
Also, removed a few similarly problematic float comparisons.
20 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 1 (MICRO), type 4 (BUG_FIX)
forgot to actually print out the computed depth
Thanks to P Taylor for noticing.
05 Feb 2024, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
change GIFTI write from PREFIX to HEADNAME
Previously, the output directories were not being used.
Thanks to eriklee (AFNI MB) for noting the problem.
11 Jan 2024, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
validate fim_now in AFNI_autorange_label
If the underlay existed in both orig and tlrc view, switching to the
view without an overlay would cause a crash.
Thanks to msh23m (AFNI message board) for noting the problem.
22 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
get a new idcode whenever a new dataset name is assigned
This deals with programs like 3dTsplit4D creating multiple datasets,
as well as programs like afni reading many similarly named files
Thanks for J Blujus for reminding of the issue.
21 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
allow nim->nvox to exceed int32_t range with NIFTI-1 output
Thanks to P Rais-Roldan for noting the discrepancy.
08 Dec 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 4 (BUG_FIX)
copy README files into build_src; use prev directory, not prefix
Thanks to D Glen for noting the missing README files.
14 Nov 2023, RC Reynolds, 3dNLfim, level 2 (MINOR), type 4 (BUG_FIX)
when creating non-bucket output, if float output, make all volumes float
Thanks to V Dinh for noting the problem.
13 Sep 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
have 1d_tool.py -write_xstim create an empty file if empty matrix
This got lost, but is needed for @ss_review_basic on rest data.
07 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
change afni/build to afni_build in OS_notes.macos_12_x86_64_b_user.txt
Thanks to spartaaa-git@github.com for pointing that out.
08 Aug 2023, RC Reynolds, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
when creating bucket output, clear time dimension
Thanks to Philip on MB for noting the problem.
21 Jul 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix help for -regress_make_corr_vols
It WAS ave corr, but as of Jan 2020, it is corr of voxels vs ave.
Thanks to D Glen for noting the discrepancy.
19 Jul 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX)
fix use of min instead of minor
Thanks to @dojoonyi for letting us know.
22 Jun 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
pass tlrc_base uvar as template
Sorry, PT.
02 Jun 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -regress_errts_prefix for surface analysis
It was missing $hemi to specify the hemisphere.
Thanks to A Gilemore for bringing up the issue.
05 May 2023, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
fix error cur_afni error if no AFNI is present
This was failing to finish setting up dot files.
27 Apr 2023, RC Reynolds, Isosurface, level 2 (MINOR), type 4 (BUG_FIX)
include updates for the 2002.08.12 MarchingCubes code base
Thanks to C Rorden for providing an updated translation.
17 Feb 2023, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
when counting events, default (with GUESS) to GLOBAL
Previously, when the user did not specify either -local_times or
-global_times, the number of events (and therefore IM regressors)
was based on local time run length, so many event regressors might
not be included.
Change the default to be based on -global_times.
If IM, warn if the user did not specify the timing type.
Thanks to M Hoptman for letting us know of the problem.
03 Feb 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
actually fail (not just warn) on inconsistent num echoes
Thanks to T Weiss bringing up the issue.
01 Feb 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
get SurfSmooth params from smrec dset
Thanks to Erin G for bringing up the issue.
03 Jan 2023, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -write_tsv_cols_of_interest with -tsv_labels
01 Dec 2022, P Taylor, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug: using -pre_matrix with -output_dir was broken.
Now internally use full path for pre_matrix (+bonus: check existence).
13 Oct 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix crash (in afni_base.py) if missing template
Thanks to R Birn for noting the problem.
13 Oct 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
okay, fix 'final DF fraction' to be wrt uncensored TRs
01 Sep 2022, P Taylor, 3dBrickStat, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug: when using '-min' with '-positive' (or sim) and no mask.
Tended to return 0 (now fixed). Thanks for mentioning, Xiaowei!
25 Aug 2022, P Taylor, 3ddelay, level 1 (MICRO), type 4 (BUG_FIX)
Make a tweak so that certain pathological cases don't scupper all others.
Thanks, D. Schwartz for pointing out this behavior.
23 Aug 2022, P Taylor, 3ddelay, level 1 (MICRO), type 4 (BUG_FIX)
Set correct dims being used from input dset in option_data struct.
Fixes report, and some internal instances (like micro/no change?).
03 Aug 2022, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
3dDeconvolve currently misbehaves when there are no events for IM
Have the program terminate with an error, until the problem is resolved.
Thanks for T Clarkson for pointing out the problem.
27 Jul 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX)
In mecho block when using m_tedana on Mac OS: fix copying tedana QC HTML.
Swap cp -> rsync, because Mac OS cp opts are diff than on Linux.
07 Jun 2022, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 4 (BUG_FIX)
Fix how the AMASK_FOCUS_* keywords apply for '-box_focus_slices ..'.
They didn't work before, but now do/should/might/perhaps/pleeeez.
18 May 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
allow for pb00 dsets in standard space
Thanks to Erik (MB audachang) for noting it.
11 May 2022, P Taylor, SurfLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
The 'mean' stat was accumulating int, not float, values.
This effective truncation/'digitizing' error should be fixed now.
10 May 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
do not add global line wrapper to QC block
Avoid line wrappers in the generation of out.ap_uvars.txt (might happen
when copy_anat dset has a very long name, for example).
Thanks to E Chang for pointing out the issue.
28 Apr 2022, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX)
afni_util.py:common_dir() : watch for the deadly JR scenario!
Thanks to J Ritchie for unconvering this, peculiar, issue.
22 Apr 2022, P Taylor, afni, level 2 (MINOR), type 4 (BUG_FIX)
The '-bysub ..' opt wasn't working, because a 'find' cmd was bad.
Reformatted the 'find', though it might still benefit from other tweaks.
14 Apr 2022, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 4 (BUG_FIX)
Replacement was not occurring if ROIs were purged by modal smoothing.
Fixed that bug, hopefully improving robustness to such error in future.
01 Apr 2022, RC Reynolds, @radial_correlate, level 1 (MICRO), type 4 (BUG_FIX)
create ulay in all cases
20 Mar 2022, P Taylor, apqc_make_html.py, level 1 (MICRO), type 4 (BUG_FIX)
Fix display of subj ID from 'Top' button in case when subj ID starts num.
In such cases, the unicode char for next line was misinterpreted.
15 Mar 2022, RC Reynolds, afni_util.py, level 2 (MINOR), type 4 (BUG_FIX)
cast run_time_to_polort output to int, for py2.7
Thanks to P Taylor for pointing it out.
10 Mar 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in 'mecho' QC block when m_tedana used with multiple runs.
All buttons used to point to r01; now fixed.
09 Mar 2022, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Patch unfathomable problem with -permute and -covariates combined
Covariate matrices are constructed BEFORE permutation is setup, and
that caused a problem. Patched around that.
01 Mar 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix removal of spaces with -combine_opts_tedana
Thanks to J Teves for noting the problem.
28 Feb 2022, RC Reynolds, 3dZcutup, level 1 (MICRO), type 4 (BUG_FIX)
fix typo in bounds check on -keep (was backward)
Thanks to Yixiang (on AFNI MB) for letting us know.
10 Feb 2022, RC Reynolds, afni_python_wrapper.py, level 2 (MINOR), type 4 (BUG_FIX)
change import to try from afnipy first
Biowulf has old afnipy/*.py files in abin.
Thanks to P Kusmierek and P Taylor for reporting the problem.
10 Feb 2022, RC Reynolds, 3dPval, level 1 (MICRO), type 4 (BUG_FIX)
fix dealing with an unknown option
Previously warned, but forgot to skip option (or break, depending).
Change to failure.
10 Feb 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX)
The 'pythonic' should be run if matplotlib ver is >=2.2, not just >2.2.
Used incorrect comparison operator earlier. I know bc Biowulf told me so.
09 Feb 2022, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix FIR blur padding
As noted by PT, volumes were not being properly blurred near edges.
Fix edge padding to be applied for entire FIR length, not just at
full FIR offset.
06 Feb 2022, P Taylor, 3dedgedog, level 2 (MINOR), type 4 (BUG_FIX)
Fix some badness when 4D datasets are input.
Also have a better scale value, based on 3dLocalstat sigma.
29 Jan 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
do not apply -execute if no new main script
So -write_3dD_script will not -execute.
26 Jan 2022, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 4 (BUG_FIX)
Fix how -box_focus_slices opt works if one of the AMASK* keywords is used.
Previously was producing error, not recognizing it wasn't a dset.
26 Jan 2022, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 4 (BUG_FIX)
Fix how -box_focus_slices opt works in another aspect.
Now should actually be used (had to turn off internal coord selection).
24 Jan 2022, RC Reynolds, suma, level 1 (MICRO), type 4 (BUG_FIX)
fix dupe symbol (clippingPlaneFile) error for mac 12
As reported by the international man of mystery, P Kundu.
12 Jan 2022, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 4 (BUG_FIX)
Add '-save_ftype ..' opt to this script, to make @animal_warper happy.
Thanks, DRG, for pointing this out.
09 Dec 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
balls were not verified to be entirely within dset bounds
Thanks to aclyn11 (AFNI MB) for noting the problem.
09 Dec 2021, P Taylor, 3dEulerDist, level 1 (MICRO), type 4 (BUG_FIX)
Fix new -only2D opt slice selection.
Was not always getting correct planar direction; should be now.
01 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 4 (BUG_FIX)
Was getting incorrect voxel scaling along a couple axes---fixed now.
Also re-arrange functions to be easier to call from other funcs.
26 Nov 2021, RC Reynolds, 3dGrayplot, level 1 (MICRO), type 4 (BUG_FIX)
cs_pv.c: xt no longer malloc'd
24 Nov 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
make boxes tight; scale radius to voxel counts
Tighten boxes and balls to not include unrequested voxels.
Scaling the radius allows for sub-mm voxels.
17 Nov 2021, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
handle uninit and if block in debugtrace.c, suma_datasets.c
27 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Opt '-extra_qw_opts ..' had wrong name in help file, '-qw_opts ..'.
Corrected this, as well as usage.
29 Sep 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior with longnames---just needed a quote around var.
Should work now. Also update help.
31 Aug 2021, RW Cox, 3dTcorr1D/3dTcorrelate, level 2 (MINOR), type 4 (BUG_FIX)
Change labels and statcode for -Fisher option
Sir Paul pointed out that these programs didn't have the correct
statcode when the Fisher transform was ordered, and also that the labels
were confusing. Fixed it so if -Fisher was used, the statcode is FIZT vs
FICO, and the labels have 'atanh()'
22 Aug 2021, P Taylor, lib_afni1D.py, level 1 (MICRO), type 4 (BUG_FIX)
Afni1D.uncensor_from_vector() had a syntax error in one print call').
Was missing a %, now fixed.
14 Aug 2021, RC Reynolds, coxplot, level 1 (MICRO), type 4 (BUG_FIX)
remove duplicate symbols zzzplt_ and zzpltr_
Done at the behest of D Glen.
27 Jul 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix typo in cubic resampling for viewer/3dresample (afni_slice.c)
Done with P Taylor.
27 Jul 2021, P Taylor, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix typo in cubic resampling for viewer/3dresample (afni_slice.c)
Copying Rick's fix. Thanks to user 'ymao' for raising this issue on the MB
.
20 Jul 2021, RW Cox, NIML library, level 3 (MAJOR), type 4 (BUG_FIX)
NIML file: input failed if file over 2BG in size
Due to storing filesize in int/long. Fix was to make it stored in
int64_t, and fixing a few other places.
16 Jul 2021, RW Cox, AFNI driver and GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in overlay_label='xxx' driver
Someone put the terminating NUL byte in wrong place. (Whoever did that
should be beaten.)
Also added the '\newline' escape as a way to add a line break to the
overlay label string from the driver -- since control characters aren't
really allowed.
16 Jul 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
unindent EOF command terminator in example
Thanks to I Berteletti for noting the problem.
13 Jul 2021, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 4 (BUG_FIX)
fix '-separator whitespace' in the case of blank lines
Thanks to P Taylor for noting the problem.
28 Jun 2021, RW Cox, NIML, level 2 (MINOR), type 4 (BUG_FIX)
Change byte count output for NI_write_element to int64_t
And a few other functions as well. Reason: someone tried to create a 2.8
GB .niml.dset file, which caused a problem when counting up the bytes
output using a 32 bit int. Users -- what can you do with them?
22 Jun 2021, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
calm those grumpy compilers
Issues noted by P Taylor.
15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fix (never hit?), and avoid single line 'if' conds.
Latter to avoid badness in some (older?) tcsh versions.
14 Jun 2021, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 4 (BUG_FIX)
turn off local signing in crorden/dcm2niix_console/makefile
14 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Space before 'then' in if-cond; also remove all exclamations in comments.
Resolved *very* weird opt parsing on *some* old tcsh.
08 Jun 2021, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
Modify to make it work with 2D images again
Had to fix THD_fillin_once to allow for special case of nz==1
19 May 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix volreg TSNR computation in surface analysis (TSNR still in volume)
01 May 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix niml.dset suffix in the case of -regress_compute_fitts on the surface
Thanks to the all-seeing S Torrisi for noting the problem.
29 Apr 2021, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
1) Now apply any scaling to 'data' in table (wasn't scaling, before).
2) Change table def: don't abs val Mean and SEM; use opt for that.
04 Apr 2021, DR Glen, @Atlasize, @MakeLabeltable longname fix, level 1 (MICRO), type 4 (BUG_FIX)
Longnames not working in combination with labels fixed for atlases
24 Mar 2021, P Taylor, 3dBrickStat, level 3 (MAJOR), type 4 (BUG_FIX)
Fix bug: having non-full-FOV mask + perc calcs affected other calcs.
Calcs should now be consistent even with those opts used. Thanks, RCR.
13 Mar 2021, RW Cox, parser.f, level 1 (MICRO), type 4 (BUG_FIX)
non-NUL terminated FORMAT string
In Fortran-77, character strings are fixed length and filled out with
blanks -- they are not NUL terminated as in C. In one place in parser.f,
a variable FORMAT string is used (about line 709, string C_VAL) -- but
that gets passed to an f2c library function that assumes NUL terminated
string, and so a buffer overrun error can happen. This has never caused
a crash or error, as far as I know, but was detected using the gcc
-fsanitize=address option by Chris Rorden. To avoid possible error, the
Fortran line above the use of this string FORMAT sets the last character
of C_VAL to NUL.
At the same time, changes were made to the f2c library headers to
properly adapt to either 32 or 64 bit pointers. Formerly, the pointer
size was fixed to 4 bytes.
A long commentary here for a very small issue.
08 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applying NIFTI scale_slope to dset must be after setting ADN_datum
Previously, NIFTI scalars were applied only after a DSET_load().
Thanks to D Glen for reporting the issue.
06 Mar 2021, DR Glen, MNI HCP Glasser atlas regrid, level 1 (MICRO), type 4 (BUG_FIX)
Move from grid of FreeSurfer 256^3 to match MNI 2009c grid.
The FreeSurfer grid is zeropadded to 256 slices.
All values remain the same, so essentially same atlas
except memory requirements are less and easier to combine
with template-based datasets. Also works better in Draw
Dataset plugin because of the grid match. No source code
changes, just a change in the pub/dist/atlases/current
directory
06 Mar 2021, DR Glen, @AddEdge PBAR fix, level 1 (MICRO), type 4 (BUG_FIX)
PBAR fix
04 Mar 2021, RC Reynolds, 3dROIstats, level 2 (MINOR), type 4 (BUG_FIX)
fix surprising slowness
This would previously unload/mallocize/reload every time point,
possibly to free completed data. Then NIFTI input would be re-read
every time point (this might have changed due to something else).
Instead, mallocize in the first place, not per time point.
Also, avoid scaling floats by 1.0.
Thanks to C Craddock for reporting the problem.
03 Mar 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 4 (BUG_FIX)
Had an early exit from earlier debugging.
Ironic, really, that a debugging line became a bug. Go figure.
03 Mar 2021, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 4 (BUG_FIX)
On one system an instrutable error message 'Unknown user: 1~.' occurred.
This change (doublequote file name? remove EOL in backticks?) fixed it.
27 Feb 2021, DR Glen, atlas labels - remove trailing spaces, level 1 (MICRO), type 4 (BUG_FIX)
Remove trailing spaces introduced by @Atlasize
07 Feb 2021, DR Glen, clang+gcc10 macos 10.15 mods, level 3 (MAJOR), type 4 (BUG_FIX)
Lots of little code fixes to handle compiler warnings
Makefile updated and some long outstanding issues fixed
26 Jan 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
do not convert NIFTI scaled shorts to float
If slope!=0 && inter==0, pass slope as brick_fac.
Thanks to C Caballero and S Moia for reporting this.
22 Dec 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed 6 copy-and-paste errors using MRI_TYPE_maxval
Thanks to C Rorden for bringing this up and suggesting code fixes.
22 Dec 2020, P Taylor, 3dmaskave, level 2 (MINOR), type 4 (BUG_FIX)
MRI_TYPE_maxval fixed for byte case-- thanks, C Rorden!
Same fix applied in: plug_maskave.c and thd_makemask.c.
21 Dec 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
The '-orient ..' opt wasn't working-- that has been fixed.
Now user can specify table coords with this opt.
17 Dec 2020, RC Reynolds, 1dBport, level 1 (MICRO), type 4 (BUG_FIX)
guard against silent failure of int overflow for ftop
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Now, first cp+resample src to RAI; else, shft is bad for non-xyz orients.
Output warps can still apply to original orient dset fine.
17 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX)
fix use of platform.mac_ver (was there a change?)
16 Sep 2020, DR Glen, atlas label range selector, level 1 (MICRO), type 4 (BUG_FIX)
atlas labels not interpreted in range selector properly
atlas labels caused crash if selected in angle brackets on
cmdline. Also allowed for spaces in atlas labels by replacing
with underscores in command line.
01 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX)
If '-skipwarp' was used, crashed at very end (sigh).
Fixed that crash behavior; no changes in outputs.
27 Aug 2020, RC Reynolds, @diff.tree, level 1 (MICRO), type 4 (BUG_FIX)
better handling of missing trailing directory args
26 Aug 2020, P Taylor, @animal_warper, level 1 (MICRO), type 4 (BUG_FIX)
Fix case of running prog with no args.
Should show help; now it DOES show help, with no error.
21 Aug 2020, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Fix header deps of underlying progs (namely, readglob.c).
Was crashing on some NIML reading cases.
03 Aug 2020, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fix sB update when changing surf order from 0,1 to 1,0
In only the case of setting the plugin surf_A/surf_B order to 1,0, the
need to update the surf_B index was not recognized, and it stayed at 1
(instead of the requested 0).
Thanks to D Glen for reporting the problem.
31 Jul 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior file path contained dots.
Joining filenames for output now fixed.
15 Jul 2020, P Taylor, 3dVecRGB_to_HSL, level 2 (MINOR), type 4 (BUG_FIX)
Would whine when outputting BRIK/HEAD dset if -in_scal was used; fixed.
Also, moved dep of suma_suma.h -> suma_objs.h (shd be no output change).
22 Jun 2020, P Taylor, convert_cdiflist_to_grads.py, level 2 (MINOR), type 4 (BUG_FIX)
Output col grads file was *not* scaled by bvalues, as help said it would.
Fixed: now output col grads multiplied by bvalues.
22 Jun 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 4 (BUG_FIX)
The -monty opt input was being ignored.
It now has a voice.
09 Jun 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior when -xticks_off and/or -yticks_off are/is used.
Now the specified axis will really be *empty*.
03 Jun 2020, P Taylor, epi_b0_correct.py, level 1 (MICRO), type 4 (BUG_FIX)
Programming badness if user forgot to add a nec arg to an opt.
There should be no change in behavior when correct opts are added.
31 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Two bug fixes: 1) where src_prefix is defined.
2) Make sure labels/atlases of ATL|SEG followers are passed along.
20 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fix history and memory loss
19 May 2020, DR Glen, 3dBrickStat, level 1 (MICRO), type 4 (BUG_FIX)
Volume - absolute value of voxel dimensions used now
05 May 2020, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with Lock menu toggle switches
Only one controller could be clicked on at a time!
Which was caused a long time ago by the LessTif patrol,
enforcing radio behavior even if it wasn't a radio box.
Also: rearranged buttons on menu so that main stuff
is now at top, where it's more convenient.
04 May 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
fix download of test file
Thanks to Gerome on MB for reporting the problem.
28 Apr 2020, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
Patch failure to register 2D images (I hope)
Turns out the cluster-izing step added to the weight production
zeroed out the 2D images. Cheap fix = just remove isolas instead.
23 Apr 2020, RC Reynolds, to3d, level 1 (MICRO), type 4 (BUG_FIX)
allow no controller open on input of JPEG image
22 Apr 2020, P Taylor, 1dplot.py, level 1 (MICRO), type 4 (BUG_FIX)
The '-xvals ..' opt was broken, but now is fixed.
*Now* the brain can be solved.
14 Apr 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if dataset inputs had full paths, use them in proc script
Thanks to W-L Tseng for pointing out the discrepancy.
31 Mar 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX)
fix lib_system_check:self.os_dist for newer python
31 Mar 2020, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX)
grep from $HOME/.bash_profile
30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI view equivalent for epi2anat alignment fix
19 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix use of module_test_lib.py with change to new afnipy dir
12 Mar 2020, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
account for lpc+zz when checking costs for -check_flip
Thanks to R Kampe for noting the problem.
12 Mar 2020, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX)
vstat image was generated even if 'surf' block was used in AP.
Since stats_dset in this case was *.niml.dset, no image should be made.
26 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Crashing in cases of 'pythonic' APQC with no censoring.
Have fixed now.
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fix, caught by RCR. Or was it first *added* by RCR????
... Nope. It was added by me. Sigh.
24 Feb 2020, P Taylor, adjunct_make_script_and_rst.py, level 1 (MICRO), type 4 (BUG_FIX)
Fix image caption processing.
(This prog is just used in RST/documentation generation.)
21 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Crashing in cases of 'basic' APQC with no outlier-based censoring.
Have fixed now.
19 Feb 2020, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 4 (BUG_FIX)
block inappropriate 'FATAL ERROR: ... already exists'
This happened when anat_in was local and stripped, so it matched ns_pref.
Thanks to R Kampe for noting the problem.
18 Feb 2020, RC Reynolds, @Align_Centers, level 1 (MICRO), type 4 (BUG_FIX)
fix copy-and-paste error and missing endif
Thanks to R Kampe for noting the problem.
14 Feb 2020, RW Cox, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Get Atlas Colors working again
Problem: 2 generations of overlay colorization changes.
a) Overlay went from indexes to RGB
b) Overlay went from indexes or RGB to RGBA
The atlas overlaying function didn't allow for these very well,
especially the latter. Obviously, this can't be my fault since I'm the
boss - even though I wrote the offending code. Someone must have joggled
my brain.
29 Jan 2020, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had RGB type, which happens for DEC maps.
Has been fixed now.
29 Jan 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX)
The input opt '-xfile ..' was broken; now it is fixed.
Fix class inits, as well, under the hood.
27 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in QC.
Broke when there was one stim used (bad scalar -> list conv).
26 Dec 2019, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix one of the test criteria (-is_mat_even).
Thanks, S. Torrisi, for pointing this out.
27 Nov 2019, RC Reynolds, ROIgrow, level 1 (MICRO), type 4 (BUG_FIX)
if PER_NODE, also process label == 0
Thanks to K Dembny for noting the problem.
21 Nov 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 4 (BUG_FIX)
add 'endif' for if( $warpdrive_method == '3dWarpDrive'
Thanks to T Holroyd for reporting and fixing this.
21 Nov 2019, RC Reynolds, 3dRank, level 2 (MINOR), type 4 (BUG_FIX)
fix storage_mode handling (re-allow niml.dset output)
Thanks to dmoracze on the Message Board for noting the problem.
19 Nov 2019, RC Reynolds, tedana.py, level 1 (MICRO), type 4 (BUG_FIX)
add arr.flags.writeable fallback in volumeutils.py:array_from_file()
Done for L Sepeta, for CentoOS 6.
13 Nov 2019, DR Glen, AFNI Clusterize, level 2 (MINOR), type 4 (BUG_FIX)
ICent error
Couple bugs in ICent location computation - thx to Meghan Robinson
28 Oct 2019, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
fix THD_write_niml to apply directory to output file
Thanks to pmlauro on Message Board, for pointing out the problem.
21 Oct 2019, P Taylor, afni, level 1 (MICRO), type 4 (BUG_FIX)
Had named an option differently than help file stated; now renaming.
To show 'AFNI Tips', opt named: -tips.
17 Oct 2019, RC Reynolds, Makefile, level 1 (MICRO), type 4 (BUG_FIX)
for strcasestr, we need to define _GNU_SOURCE in Makefile.*
17 Oct 2019, RC Reynolds, 3dTcorr1D, level 1 (MICRO), type 4 (BUG_FIX)
strcasestr fix subsumed by adding _GNU_SOURCE to make
Undo removal of strcasestr.
15 Oct 2019, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
-bysub fix
Methods 1 and 2 can conflict, and the choice is arbitrarily made to
favor Method 1 when the input matches both situations.
10 Oct 2019, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
search for niml.dset errts datasets
10 Oct 2019, RC Reynolds, afni_base.py, level 1 (MICRO), type 4 (BUG_FIX)
in NIML case, exist should check ppv file directly
04 Oct 2019, RC Reynolds, 3dNLfim, level 1 (MICRO), type 4 (BUG_FIX)
allow for longer input and output file names
Names were malloc'd with MAX_NAME_LENGTH; use nifti_strdup, instead.
Thanks to S Wardle for bringing this to light.
23 Sep 2019, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
missed endif
Thanks to A Winkler for noting the problem.
31 Aug 2019, DR Glen, @animal_warper,@FindAfniDsetPath, level 1 (MICRO), type 4 (BUG_FIX)
better full_path option for paths with ../
More use in animal_warper for templates and atlases
31 Aug 2019, DR Glen, @animal_warper, level 1 (MICRO), type 4 (BUG_FIX)
follower fixes
30 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix input opt to change blur size; was broken before, crashing prog.
Thanks, L. Dowdle for finding!
23 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed calculation when PE effective echo spacing is input.
The conversion to BWPP was wrong; led to almost no distortion corr.
22 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
(w/dglen) thd_gifti: remove INDEX_LIST DA from from list
When converting a GIFTI dataset to NIML, any index list should be
separated early, so as not to affect the SPARSE_DATA NIML element.
Thanks to T Holroyd for noting the problem.
19 Aug 2019, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 4 (BUG_FIX)
matrix_f.[ch]: dupe matrix_augment_01_columns from matrix.[ch]
When choosing between more local functions and those included in a
linked library, some systems seem to go all-or-nothing for one file
at a time. So for 3dDeconvolve_f, matrix_f.c needs everything that
might come from matrix.c. Otherwise we should have matrix_f.h rename
all of those functions, to avoid relying on compiler choices.
16 Aug 2019, JK Rajendra, FATCAT_matplot, level 1 (MICRO), type 4 (BUG_FIX)
Fix for FATCAT_matplot header reading.
13 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
fix -VXXXX= for real operating systems
29 Jul 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Reduce colorization interpolation problem
When using discrete panes, conversion to 'continuous' colorscale causes
a problem right at the boundary. This change reduces this problem.
22 Jul 2019, DR Glen, @Install_D99_macaque,NIH_Marmoset, level 2 (MINOR), type 4 (BUG_FIX)
download script bugs
tar platform differences and filename updates
19 Jul 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
if template is multi-volume, get vol [0] for group_mask
Thanks to S Tumati for noting the problem.
18 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Hadn't merged in updated library functions, so apqc_make_tcsh.py crashed.
Updated library file in distribution now.
18 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 4 (BUG_FIX)
Used to crash if output dir was PWD.
Now fixed.
17 Jul 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
another fix for 32-64 bit NIFTI update for older xorg7 systems
In thd_niftiread.c, cast nim->nz as int for EDIT_dset_items().
Newer C libraries seem to handle the possibility of 8 bits better,
but we are reading as 4. Thanks again to R Birn.
17 Jul 2019, RC Reynolds, NIFTI, level 1 (MICRO), type 4 (BUG_FIX)
fix inappropriate 'dimensions altered' warning on xorg7
Warning: dimensions altered since AFNI extension was added
Use PRId64 for 64-bit int printing, works on old systems, too.
Thanks to R Birn for noting the problem.
16 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix incompatibility with py2.
Sigh.
03 Jul 2019, RC Reynolds, 3dvolreg, level 1 (MICRO), type 4 (BUG_FIX)
make 'second -zpad option' warning appropriate again
03 Jul 2019, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
allow writing of empty stim files ($status 0)
20 Jun 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 4 (BUG_FIX)
Use the CAPTION feature on image tables in text blocks.
Also fix help display.
19 Jun 2019, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
AFNI_PBAR_THREE mode didn't allow proper change of the panes
Problem: code to put labels on the panes being invoked when it shouldn't
be. Ugh. Who wrote this code, anyway? They should be SHOT!!
18 Jun 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
no mask if TSNR on surface
Thanks to K Dembny for noting the problem.
06 Jun 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Different fix for the threshold scale size problem :(
04 Jun 2019, RC Reynolds, plug_tag, level 2 (MINOR), type 4 (BUG_FIX)
use calloc to init last 4 bytes of tag string in thd_dsetatr.c
This was leaving garbage in HEAD file.
Thanks to A Nugent for noting the problem.
23 May 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Would not run in python2, because of subprocess.run() call (only py3).
Now updated to using afni_base.py functions to execute shell cmds.
20 May 2019, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
modify pane_scale to match updates for AFNI_PBAR_FULLRANGE
18 Apr 2019, DR Glen, whereami GUI with wrong atlas, level 1 (MICRO), type 4 (BUG_FIX)
whereami would crash afni GUI if atlas was not found
Also more descriptive message when no available atlases
16 Apr 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
verify av_space == +tlrc before setting template
Thanks to P Molfese and P Taylor for noting the problem.
29 Mar 2019, RW Cox, @SSwarper, level 1 (MICRO), type 4 (BUG_FIX)
Strip dataset suffixes from -subid input
Otherwise, using '-subid Fred+orig' will cause trouble, for example. Or
'-subid Fred.nii' will work, but produce output files with names ending
in '.nii.nii' which is confusing.
20 Mar 2019, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 4 (BUG_FIX)
sync crorden/dcm2niix_console with repo, version v1.0.20181125
This is possibly to correct a bug with -m and partial brain coverage.
15 Mar 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Better behavioring of -box_focux_slices when ulay and refbox grids differ.
Now checking grid similarity and resampling refbox if needbe.
08 Mar 2019, RW Cox, InstaCorr, level 2 (MINOR), type 4 (BUG_FIX)
Bandpass error found by the wandering Spaniard
Problem: very long time series (over 2000) analyzed *without* Bandpass
would give error message and then give useless results.
Solution: if Bandpass is turned off, that is signaled by setting the
upper freq cutoff to a large value. Then the FFT cutoff index is
computed from that as jtop = ftop/df where df = 1/N*dt, so we have
jtop = ftop*N/dt. For large N and large ftop, this is integer overflow.
Therefore, compute jtop in float, not int, then check it first. D'oh.
04 Mar 2019, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
-superhard did not imply -workhard :( -- now it does :)
28 Feb 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
mask dset must include extension
05 Feb 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX)
allow -extent to vary across datasets
05 Feb 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Had been missing an endif.
Now new and improved-- with endif!
04 Feb 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
use abs in dims check for -mask_import
25 Jan 2019, P Taylor, @djunct_slice_space, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had subbrick selectors from @chauffeur*.
Has been fixed now.
25 Jan 2019, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had subbrick selectors from @chauffeur*.
Has been fixed now.
19 Jan 2019, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX)
Program wouldn't run with '-odir ..' opt.
Now it will.
21 Dec 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Adjusted coordinator for a couple situations.
Should be more centered for both 3D and 4D applications.
19 Dec 2018, P Taylor, @djunct_montage_coordinator, level 3 (MAJOR), type 4 (BUG_FIX)
This montage coordinator was noooot picking the right vol to focus on.
That should be fixed via magical incantations now.
11 Dec 2018, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
use mkdir -p; reconcile write_as_nifti and NIFTI prefix
Thanks to C Smith for noting the issue.
02 Dec 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Will work with resting state analyses now.
Fixed minor issue when no stat dset (just NO_STATS str) was present.
28 Nov 2018, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX)
In py3, having a censor line caused graphing issues.
Those issues have been resolved.
27 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Wasn't using user's specified delta_slices-- but now is!.
Grazie, S. Torrisi!
25 Nov 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX)
Dsets weren't found in places specified by env var.
Fixed now.
20 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Fixed the calc of the location of xhairs when box_focus_slices was used.
Should have correct focal location in montages now.
06 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Fixed delta-slice definition for 4D mode of imaging (occasional probs).
Should have correct gapord values across all views now.
16 Oct 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX)
Maybe not really a bug, but this program wasn't work as it should have.
It now should find NIFTI sets better, and use afnirc env vars.
09 Oct 2018, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
fix decay rest with non-zero min; block unlimited decay stim dur
Thanks to D Plunkett for noting the problem.
04 Oct 2018, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
wget/curl may remove execute permission, so re-add it
25 Sep 2018, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
fix first timediff in -multi_timing_to_event_list
20 Sep 2018, RC Reynolds, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
fix copy-and-paste error for processing of voxelwise covariates
Use of voxelwize covariates when only using -setA was crashing.
Thanks to S. Kippenhan for noting the problem.
12 Sep 2018, RC Reynolds, 3dClusterize.c, level 1 (MICRO), type 4 (BUG_FIX)
fix limit check on -idat and -ithr; disable MMAP for input
10 Sep 2018, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 4 (BUG_FIX)
add (copy of) Audio directory to afni_src.tgz build target
14 Aug 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX)
return a zero array on invalid parameters
Thanks to E Silson for noting the problem.
13 Aug 2018, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
actually apply opt -blur_opts_BIM
Thanks to D Zhu for noting the problem.
10 Aug 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
Allow non-stat bricks to be thresholded.
Before, if the [ithr] brick was nonstat, crashing occurred.
07 Aug 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if converting tedana.py results to standard space, include -space
Thanks to L Dowdle for noting the problem.
01 Aug 2018, P Taylor, @chauffeur_afni, level 1 (MICRO), type 4 (BUG_FIX)
Deal correctly with percentile values for 4D ulay in non-4Dmode...
... because user may specify with subbrick selectors.
25 Jul 2018, P Taylor, @djunct_calc_mont_dims.py, level 2 (MINOR), type 4 (BUG_FIX)
Was excluding solution of a square set of dimensions.
Tested; seems fine now.
26 Jun 2018, P Taylor, fat_proc_select_vols, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixed in supplementary program to *this* program.
Used to get an error when no bad vols were selected.
26 Jun 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 4 (BUG_FIX)
Would return an error when *no* bad vols were selected.
Note about fixing it in Jan, 2018; must have forgot to push that ver!
19 Jun 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX)
fix rotation term, B should be 2*B
Thanks to R Le, G Usabiaga and B Wandell for suggesting a review.
08 Jun 2018, RC Reynolds, 3ddata.h, level 1 (MICRO), type 4 (BUG_FIX)
have DUMP_MAT44 write to stdout again (might re-do stderr later)
Need to fix align_epi_anat.py for stderr, but must check shell use.
Thanks to T Radman for noting the problem.
30 May 2018, P Taylor, @suma_reprefixize_spec, level 1 (MICRO), type 4 (BUG_FIX)
Changing 'more' -> 'cat', internally.
Think 'more' gave oddness at times- dumped weird chars and broke files.
22 May 2018, P Taylor, fat_proc_filter_dwis, level 3 (MAJOR), type 4 (BUG_FIX)
Was unioning, not intersecting, multiple selector strings.
Fixed the issue in subprogram @djunct_combin_str.py.
14 May 2018, RC Reynolds, afni.c, level 1 (MICRO), type 4 (BUG_FIX)
check at 'only if do_css' should be css, not gss
Without GLOBAL_SESSION, this blocked the All_Datasets session.
13 May 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
Wouldn't work with extra dset entered- fixed now.
Can enter extra beta/effect estimate set for clusterizing.
09 May 2018, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix 'too many redraws' problem in imseq.c
For some reason, could get many ConfigureNotify events for one image
resize, each event causing a redraw. Now if the redraw ordered by a
ConfigureNotify is exactly the same size as the previous one, it will be
skipped.
08 May 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
3dQwarp warp datasets need only be named _WARP
Thanks to dowdlelt on MB for bringing this up.
29 Apr 2018, DR Glen, First space xform bug, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug where first space in AFNI_atlas_spaces.niml had to have xform
25 Apr 2018, RC Reynolds, meica.py, level 2 (MINOR), type 4 (BUG_FIX)
deal with numpy update that fails for 'array == None', use 'is None'
Thanks to dowdlele on MB for noting this and pointing to the emdupre
update on https://github.com/ME-ICA/me-ica.
22 Apr 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 4 (BUG_FIX)
When using '-remove_inf_sli', the wrong volume was being warped at end.
Final warped volume had lower slice reduction, when it shouldn't have.
04 Apr 2018, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
set sysname early - forgot to commit this weeks ago...
14 Mar 2018, P Taylor, fat_proc_filter_dwis, level 2 (MINOR), type 4 (BUG_FIX)
Crashed when b-value file was input.
Crashes no more under such circumstance.
14 Mar 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 4 (BUG_FIX)
Crashed no ref dset was used in mapping.
Crashes no more under such circumstance.
07 Mar 2018, RC Reynolds, afni, level 1 (MICRO), type 4 (BUG_FIX)
add do_css check around css access for making catenated session list
08 Feb 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 4 (BUG_FIX)
When a mask was input, it wasn't resampled if needed to be.
Now fixed, and added check that grid of mask is good. Good.
28 Jan 2018, DR Glen, @measure_xxx surface object controllers, level 1 (MICRO), type 4 (BUG_FIX)
keep surface object controllers open in the output suma scripts
Mac OS bug makes closing and reopening controllers crash
26 Jan 2018, RC Reynolds, dicom_hinfo, level 1 (MICRO), type 4 (BUG_FIX)
fix crash on no input file
26 Jan 2018, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
applied various NeuroDebian patches from M Hanke and Y Halchenko
Includes up_include_right, up_condition_dset_unload, up_3dNetCorrFix,
and up-fix_inflate_compare.
Thanks to M Hanke and Y Halchenko for the fixes.
12 Jan 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 4 (BUG_FIX)
Would return an error when *no* bad vols were selected.
Now updated to work fine with that; just an intermed program.
12 Jan 2018, P Taylor, fat_proc_align_anat_pair, level 1 (MICRO), type 4 (BUG_FIX)
Output 3dAllineate's weight vol to working dir, not present dir.
Minor change, does not affect alignment/output.
27 Dec 2017, RC Reynolds, RetroTS.py, level 1 (MICRO), type 4 (BUG_FIX)
prevent slice_order = 'Cutsom' case from wiping out passed order
Thanks to J. Ho for noting the problem in the Matlab version.
20 Dec 2017, RW Cox, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Make -substatpar option work better
It didn't work on some datasets, as they weren't labeled as 'bucket'.
That oversight was fixed.
11 Dec 2017, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 4 (BUG_FIX)
in dilate, if pad but not convert, inset == dnew, so do not delete
Thanks to nwlee (AFNI message board) for noting the problem.
04 Dec 2017, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fix gtmax in case of global times and only 1 input dset
This just lead to an inappropriate warning.
Thanks to P Bedard for noting the problem.
30 Nov 2017, RC Reynolds, afni_base.py, level 1 (MICRO), type 4 (BUG_FIX)
fix problems with relative path to root directory
This affected afni_proc.py, for example, adding '/' in path names.
Thanks to D Nielson for noting the problem.
27 Nov 2017, RC Reynolds, afni, level 1 (MICRO), type 4 (BUG_FIX)
fix imseq.c: driven SAVE_MPEG offset by 1
15 Nov 2017, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
-despike_mask had been tested with wrong option name
Fix submitted by D Plunkett.
12 Oct 2017, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fixed color def problem in pbars (etc) with new find_color_name func
27 Sep 2017, RW Cox, 3dXClustSim, level 1 (MICRO), type 4 (BUG_FIX)
Ooops: modify to have different min thresholds for each FPR goal
22 Sep 2017, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 4 (BUG_FIX)
On Macs, when not all types of 'follower' sets were used, this gave err.
Have changed internal behavior to avoid this 'Mac'errorizing.
19 Sep 2017, P Taylor, 3dLombScargle, level 2 (MINOR), type 4 (BUG_FIX)
delF calculated correctly now.
Had been at N-1 instead of N. Better Parsevalling now.
14 Sep 2017, P Taylor, 3dLombScargle, level 3 (MAJOR), type 4 (BUG_FIX)
Finally revisiting this-- fixed up lots of things.
Good to go for basic functionality now.
06 Sep 2017, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
re-apply cleaner xim use, so end of run signal has full image size
Short end of run was hanging afni, but was not noticed since the
communication was immediately terminated. Fixes multi-run use.
30 Aug 2017, RC Reynolds, model_conv_PRF, level 1 (MICRO), type 4 (BUG_FIX)
determine NT restriction based on reorg
Was limited to NT. Applies to PRF, PRF_6, PRF_DOG
Thanks to E Silson for noting the problem.
08 Aug 2017, P Taylor, 3dTrackID, level 1 (MICRO), type 4 (BUG_FIX)
More specific glob for 3D vol files *only*; had gotten 1D text in list.
Getting 1D text files would throw error. More specific search now.
04 Aug 2017, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
-ETAC failed without multiple blur cases
Addition of -ETAC_blur broke the non-blur runs, due to lack of the
correct 'label' for dealing with the results from 3dXClustSim.
Obviously, this was the work of saboteurs.
27 Jul 2017, RC Reynolds, 3dNwarpApply, level 1 (MICRO), type 4 (BUG_FIX)
fix memory alloc for warp file names
Thanks to L Lebois (and others on MB) for noting the problem.
19 Jul 2017, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
adjust looking for good stim times to handle global timing
Max time was previously that of the longest run. For global timing,
accumulate across runs.
Thanks to B Callaghan, Michael, ace327 and Jeff for noting the problem.
15 Jun 2017, RC Reynolds, uber_subject.py, level 1 (MICRO), type 4 (BUG_FIX)
handle empty subj_dir
05 Jun 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
peak_finder(): fix lengths of r['t'] and r['tR']
Be more cautious with ratios that are very close to integers.
05 Jun 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
merge phase_base() fix by D Nielson
range() is closed in matlab but half-open in python.
26 May 2017, P Taylor, 3dReHo, level 2 (MINOR), type 4 (BUG_FIX)
Correct checking for null time series now.
Earlier, only looked at [0]th point; now sums across all.
26 May 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 4 (BUG_FIX)
Correct checking for null time series now.
Earlier, only looked at [0]th point; now sums across all.
17 May 2017, RC Reynolds, RetroTS.py, level 1 (MICRO), type 4 (BUG_FIX)
D Nielson's fix in PeakFinder.py dealing with non-integer subscripts
Required by latest version of numpy.
11 May 2017, P Taylor, 3dDTtoDWI, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed mismatch in multiplying DT and bmatrices.
Element indices hadn't been sync'ed, now they are.
09 May 2017, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
if to3d_prefix is NIFTI, clear write_as_nifti
Thanks to A Nugent for noting the problem.
02 May 2017, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
properly handle column major order
Convert to row major order on read; can control with gifti_tool.
Thanks to JH Lee for noting the problem.
26 Apr 2017, RW Cox, 3dXClustSim, level 1 (MICRO), type 4 (BUG_FIX)
Bug in looping index in STEP 2 caused malloc() problems. Oog
25 Apr 2017, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix follower warps for gzipped NL-WARP datasets
Thanks to C Connely for noting the problem.
12 Apr 2017, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
in suggest_best_prog_option(), do not search for -help, -h_* or similar
A program without -help that tests it would otherwise lead to an
infinitely recursive system call trying to use -help to suggest an option.
05 Apr 2017, RC Reynolds, uber_subject.py, level 1 (MICRO), type 4 (BUG_FIX)
apply subject dir again; allow -cvar subj_dir to override default
30 Mar 2017, P Taylor, lib_fat_funcs.py, level 1 (MICRO), type 4 (BUG_FIX)
An error message in func called by fat_mvm_scripter.py was wrong.
Fixed an indexing mistake which gave wrong ROI list-- thanks, E. Grodin!
27 Mar 2017, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
rm of temporary files could delete all files in current directory
rm deletes all files that have tabs/spaces inserted in dataset names
The tab or space character can be somewhat invisible if after
line continuation character in input script. Fix removes whitespace
before deleting
21 Mar 2017, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Improper fading of overlay plots in Montage
function scale_memplot() was scaling the opacity factor as well as the
xy coordinates - D'oh!
21 Mar 2017, RC Reynolds, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
fix projection of surfaces with non-zero centers
Center each surface around 0,0,0 instead of leaving the offset in.
Many thanks go to I Dewitt for even noticing this subtle issue,
much less diagnosing where it might be coming from. Not easy.
21 Mar 2017, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
allow for volreg-only script with MIN_OUTLIER
21 Mar 2017, RC Reynolds, @FS_roi_label, level 1 (MICRO), type 4 (BUG_FIX)
extra quote on line: choose one of $lbls
07 Mar 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
from J Zosky: default to using numpy.flipud()
The flipud() function did not work in the original Matlab version,
but it does in numpy. Use the new -legacy_transform opt for old
(and presumably incorrect) results.
06 Mar 2017, RC Reynolds, AFNI.afnirc, level 1 (MICRO), type 4 (BUG_FIX)
AFNI_COMPRESSOR can be set to GZIP, not gzip
20 Feb 2017, RW Cox, 3dDespike, level 2 (MINOR), type 4 (BUG_FIX)
Scale factor bug
The program ignored the scale factors attached to short datasets.
If they were all the same, that was not a problem.
But if they differed, then that was a big problem.
That was fixed. Also, the output now is always in float format.
09 Feb 2017, P Taylor, @GradFlipTest, level 1 (MICRO), type 4 (BUG_FIX)
Some IF conditions gave problems; some option names were inconvenient.
They are now ex-parrots.
23 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 4 (BUG_FIX)
allow automatic use of the INSTANT timing class
19 Jan 2017, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fix for -final_anat
Thanks to N Anderson for noting the problem.
05 Jan 2017, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI output and output directories not always handled correctly or completely
29 Dec 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
remove case 16 (brainstem) from aparc+aseg.nii WM extraction in help
Thanks to P Taylor for noting this.
23 Nov 2016, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Used to be able to have nans in sBL b/c of sqrt(neg-from-rounding).
Now IF condition to prevent that. Happy Thanksgiving.
23 Nov 2016, P Taylor, 3dNetCorr, level 2 (MINOR), type 4 (BUG_FIX)
Z-score WB maps were all zeros-> now have values.
Hopefully even the correct Z-values.
16 Nov 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 4 (BUG_FIX)
The -out_bval_col_sep used did nothing (after last changes).
Have returned it to functionality.
08 Nov 2016, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
possibly invert slice order, as DICOM sorting might affect MRILIB_orients
Thanks to W Luh for noting the problem.
03 Nov 2016, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Single slice dataset InstaCorr failed
Due to the 'roundtrip' index calculation giving a value outside the
dataset. This is now prevented.
13 Oct 2016, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fix -BminusA bug
double sign reversal == no sign reversal == not good for anyone
31 Aug 2016, P Taylor, 3dSpaceTimeCorr, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug in yet-unreleased function... and also changed a feature.
Bug: ts = all0 -> GSL badness on some comp; now, exclude seedvox in corr.
25 Aug 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix output.proc prefix in case -script has a path
Also, allow -mask_apply group in the case of -tlrc_NL_warped_dsets.
Thanks to C Capistrano and P Kim for noting the output.proc problem.
Thanks to C Connolly for noting the mask problem.
19 Aug 2016, DR Glen, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
Neighborhoods miscalculated
18 Aug 2016, P Taylor, 3dReHo, level 2 (MINOR), type 4 (BUG_FIX)
Used to not allow subbrik selection on input.
Now it does. Thanks to Daniel H. for pointing it out.
17 Aug 2016, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
History not updated properly on output with NIFTI dset1/anat
06 Aug 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
mri_read_ascii: check comment_buffer before strdup
01 Aug 2016, P Taylor, 3dRSFC, level 2 (MINOR), type 4 (BUG_FIX)
In cases of *very large* N_pts, an error message appeared-- no more.
Just changed default initialization of >f_N value.
25 Jul 2016, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed attaching lone '-' to following label
No NI_malloc might lead to crash, and the '-' was overwritten.
14 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with -resid combined with -clustsim
Program assumed prefix_resid was NIFTI format,so just add '.nii' if it doe
s have that already.
14 Jul 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_tcat: print error and return NULL on bad wildcard match
11 Jul 2016, DR Glen, 3dWarp tta2mni grid dimensions bug, level 2 (MINOR), type 4 (BUG_FIX)
Ignored grid dimensions in transformation between Talairach to MNI
30 Jun 2016, DR Glen, unWarpEPI.py anat to epi lpc+ZZ cost, level 2 (MINOR), type 4 (BUG_FIX)
Mistakenly used lpa for anat to epi alignment
29 Jun 2016, RC Reynolds, 3dfim, level 1 (MICRO), type 4 (BUG_FIX)
fix crash for dset open error with long dset name
Thanks to J Henry for reporting the problem.
29 Jun 2016, DR Glen, align_epi_anat.py flipping identity, level 2 (MINOR), type 4 (BUG_FIX)
Case of mistaken IDENTITY for check_flip option
22 Jun 2016, RC Reynolds, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
correctly check base.exists()
20 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 4 (BUG_FIX)
Fixing bug in delta F calculation.
What more needs to be said?
19 Jun 2016, DR Glen, align_epi_anat.py dset1/2 deobliquing, level 1 (MICRO), type 4 (BUG_FIX)
Using dset1/2 terminology forced deobliquing off
17 Jun 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
w/dglen, dsets with HEAD in prefix (but no suffix) could not be opened
16 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if NLwarp but no EPI warp, no NL; fix refit of blip median datasets
User probably forgot -volreg_tlrc_warp, so warn them.
14 Jun 2016, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
Conversion to vector image fails for LARGE datasets
The final step in the conversion to vectim is scanning the data for
floating point errors (NaN, infinity). If there are more than 2^31-1
voxels, integer overflow caused problems. Fixed by making the loop
variables in the floatscan functions be size_t, not int. This problem
certainly lurks elsewhere in AFNI, waiting to pounce on Spaniards.
03 Jun 2016, DR Glen, 3dQwarp bug, level 2 (MINOR), type 4 (BUG_FIX)
bug fix in option processing
Fixed wtprefix handling and gridlist option handling (with RCR)
19 May 2016, RC Reynolds, dicom_hdr, level 1 (MICRO), type 4 (BUG_FIX)
do not crash on missing input
17 May 2016, RW Cox, 3dUnifize, level 1 (MICRO), type 4 (BUG_FIX)
-ssave option caused a crash :-(
fixed in Hangzhou China
04 May 2016, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
-dsort always produced the _nods dataset; now, only if -nods is used
03 May 2016, DR Glen, whereami - atlas queries, level 1 (MICRO), type 4 (BUG_FIX)
Removing structures that are all numbers was breaking atlas label queries
25 Apr 2016, DR Glen, afni GUI perc threshold flag, level 1 (MICRO), type 4 (BUG_FIX)
percentile thresholding didn't work properly with warp-on-demand between views
19 Apr 2016, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
incorrectly reported 'IFM:RIF fatal error' for the case of no sorting
Thanks to I Groen for reporting the problem.
18 Apr 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_tcat: fix wildcard input lacking sub-brick selectors
Forgot to regenerate catenated list, dlocal.
04 Apr 2016, RC Reynolds, THD_load_tcat, level 2 (MINOR), type 4 (BUG_FIX)
set factors and labels at open time, not at load time
This fixes use with 3dcalc and 3dinfo, though stats are not yet loaded.
26 Mar 2016, RC Reynolds, to3d, level 1 (MICRO), type 4 (BUG_FIX)
another allowance for datasets exceeding 2 GB
Thanks to SS Kim for noting the problem.
21 Mar 2016, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
get slightly more accurate motion ave via 3dTstat -nzmean
17 Mar 2016, RW Cox, 3dTproject, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem in setting count of bandpass regressors
Typo meant that Nyquist frequency might not be counted properly,
resulting in bad stuff (memory corruption).
15 Mar 2016, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
-help_basis update: max convolved BLOCK() is ~5.1, not ~5.4
07 Mar 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed edge option change using too small neighborhood size
01 Mar 2016, RC Reynolds, GIFTI, level 1 (MICRO), type 4 (BUG_FIX)
applied R Vincent fix for GIFTI datasets with Windows-style newlines
24 Feb 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -warn_tr_stats crash on empty timing file
Thanks to Z Reagh for noting the problem.
10 Feb 2016, RC Reynolds, @ANATICOR, level 1 (MICRO), type 4 (BUG_FIX)
fixed -radius option parsing
Thanks to A Frithsen for noting the problem.
10 Feb 2016, DR Glen, afni, level 1 (MICRO), type 4 (BUG_FIX)
fixed ignoring of -no1D option, and 1D files are not read on input
09 Feb 2016, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
be sure isfinite is defined in FD2_inc.c, parser_int.c
05 Feb 2016, RC Reynolds, thd_niftiread, level 1 (MICRO), type 4 (BUG_FIX)
NIFTI files with no *form_codes should default to +orig, not NIFTI_default
22 Jan 2016, DR Glen, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
skip_affine option previously skipped
22 Jan 2016, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Incorrect check for file output existence for oblique data
04 Jan 2016, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
add boundardy checks in get_1dcat_intlist and get_count_intlist
Without the checks, using count or 1dcat as sub-brick selector method
would lead to confusing crashes (if values exceeded #vols).
Thanks to W Graves for reporting the problem.
04 Jan 2016, P Taylor, 1dDW_Grad_o_Mat, level 1 (MICRO), type 4 (BUG_FIX)
Fixed backwards output messages.
Should now be easier to see what went bad in a case of mistaken input.
31 Dec 2015, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Don't allow -resid and -zskip at the same time
Because sorting out the residuals back to their proper places would
be hard, if some inputs were skipped.
31 Dec 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
include AFNI_version_base.txt in build of afni_src.tgz
29 Dec 2015, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX)
catch any empty directory listing from @FindAfniDsetPath
07 Dec 2015, RC Reynolds, MatAFNI_Demo.m, level 1 (MICRO), type 4 (BUG_FIX)
merge fix from J. Pfannmoller
Done with G Chen.
28 Sep 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Use list of ROIs to select subnetwork of analysis for 3dMVM.
Previously, sublist only applied to post hocs, not 3dMVM models.
18 Sep 2015, DR Glen, @DBSproc bug fix, level 2 (MINOR), type 4 (BUG_FIX)
Left-right coordinate flip in @DBSproc script for Silvina Horovitz
11 Sep 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
edt_floatize.c: for NIFTI float->float with scale factors, apply them
Also, fix determination of when to convert.
Thanks to Pengmin (MB) for noting this problem.
10 Sep 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix resulting aligned SurfVol if input is NIFTI
09 Sep 2015, RW Cox, whereami (etc), level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in parsing LinkRbrain output XML file
Problem: fread() of file does not NUL terminate the string -- causes
problems! Simply solved.
Also fixed problem in afni_cluster.c, where peak coords and cmass coords
passed to LinkRbrain were being interchanged.
02 Sep 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
some option vars were being over-written
28 Aug 2015, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Hack to allow -stim_times_IM to work with times > TMAX
Times > TMAX are ignored. In usual cases, this isn't a problem. But
with IM regression, each time gets a regressor, and times > TMAX produce
all zero regressors -- which is a problem. This hack will cut them off
(at least in some cases).
21 Aug 2015, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
start-of-run fix to -multi_timing_to_event_list offsets
14 Aug 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
SUMA_CIFTI_2_edset: use 'no suma' version: SUMA_WriteDset_ns
09 Aug 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when GM map has no ROIs/clusters.
No more crashing... Won't produce GM or GMI volumes; message only.
07 Aug 2015, RC Reynolds, model_conv_PRF_6, level 1 (MICRO), type 4 (BUG_FIX)
make everything static, to avoid confusion; proto for conv_set_ref
05 Aug 2015, P Taylor, fat_mvm_prep.py, level 1 (MICRO), type 4 (BUG_FIX)
Micro ~bug fixed for inputting CSV headings.
Now strip off lead/trail whitespace, then replace rest with underscore.
03 Aug 2015, RC Reynolds, Dimon1, level 1 (MICRO), type 4 (BUG_FIX)
fixed -drive_afni, -drive_wait and -rt_cmd command lists
03 Aug 2015, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
applied ACQUSITION_TYPE as 3d+timing
Slice timing was lost (by the plugin) in the change to 3d+t ACQ TYPE.
Thanks to H Mandelkow for bringing this up.
30 Jul 2015, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 4 (BUG_FIX)
check for template existence even given path
Was failing with -init_xform.
24 Jul 2015, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
GIFTI datasets should have NODE_INDEX list as first DataArray
Thanks to N Oosterhof for pointing this out.
22 Jul 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when refset has negative values.
No more crashing...
17 Jul 2015, RW Cox, mri_write.c, level 1 (MICRO), type 4 (BUG_FIX)
Make mri_write_1D("stdout:") work correctly
Before you could get filename "stdout:.1D" which is not very useful.
14 Jun 2015, DR Glen, align_epi_anat.py edge, level 1 (MICRO), type 4 (BUG_FIX)
Fixed broken edge option
10 Jun 2015, RC Reynolds, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
clear any AFNI_COMPRESSOR variable, so that scripts do not get confused
NIFTI is the default, so avoid script confusion with automatic nii.gz.
In the future, maybe process as AFNI.
10 Jun 2015, RC Reynolds, NIFTI, level 1 (MICRO), type 4 (BUG_FIX)
THD_open_one_dataset: let THD_open_nifti look for alternate files
CHECK_FOR_DATA() requires a file name match, but NIFTI is forgiving.
27 May 2015, RC Reynolds, @Install_TSrestMovieDemo, level 1 (MICRO), type 4 (BUG_FIX)
set and applied $demo as Suma_TSrestMovieDemo
21 May 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fixed for inputting sublist of ROIs.
Short option for doing so worked, but not the long one; fixed now.
08 May 2015, RW Cox, InstaCorr, level 1 (MICRO), type 4 (BUG_FIX)
Change way index in 3D+time dataset is chosen from xyz
Instead of just converting from xyz (eg, crosshair) coordinates via the
standard grid transformation functions in thd_coords.c, what we want is
the voxel in the 3D+time dataset that is closest in 3D to the xyz
location AFTER it is transformed back to the underlay for display. In
this way, the center of correlation will map to the clicked voxel. This
selection is done in new function THD_find_closest_roundtrip() which
searches the 27 points in a cube around the thd_coords.c derived point,
in order to find the voxel in the 3D+time dataset that, when transformed
back to the underlay dataset, is closest. Brute force, but that's what
you have to do when dealing with the Spanish Inquisition.
27 Apr 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed output when byte/short insets were used.
Had been not writing data; needed to null brick_facs in outsets.
23 Apr 2015, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix Aux.Dset button crash in Clusterize
Because Ziad Saad is trouble, that's why.
(Either that, or 'free(x)' should imply 'x=NULL'.)
Also, catch SIGABRT signal, so Mac malloc() errors are tracebacked.
22 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
put in cat_matvec string to create warp.all.anat.aff12.1D
Thanks to sgreen (MB) for noting the problem.
15 Apr 2015, ZS Saad, suma-general, level 3 (MAJOR), type 4 (BUG_FIX)
Turned off USE_XOR for now.
Was causing very mysterious problem with labels displaying atop each other
in the SUMA viewer. Possibly other problems too like crash when opening
surface controller or changing threshold. No time to get to the bottom
of this at this time. But turning this off fixed problem on linux and osx.
Valgrind had nothing to complain about...
14 Apr 2015, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix index text overlay clash in graph window
Because Daniel Glen is trouble, that's why.
13 Apr 2015, RW Cox, AFNI itself, level 1 (MICRO), type 4 (BUG_FIX)
Fix crash when ClustSim info in dataset header is incomplete
Problem was if mask string was missing, it tried to read the
mask idcode from a now-deleleted NIML element -- bad news.
09 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix -tlrc_NL_warped_dsets for NIFTI anat; add some -regress_ROI_PC help
07 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
TLRC_warped_dsets: no view update if type != BRIK
02 Apr 2015, RC Reynolds, rickr/Makefile, level 1 (MICRO), type 4 (BUG_FIX)
Imon and serial_helper should not use LLIBS
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed syntax for env SUMA_VO_InitSlices, space chars are bad.
27 Mar 2015, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
linux_xorg7_64 distribution gets argv[nopt] wrong?!
Fixed by putting in a debug printout statement for argv[nopt] at start
of loop over options. Even when not used, this fixes the problem --
probably caused by the gcc optimizer.
23 Mar 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 4 (BUG_FIX)
Fixed projection error in SUMA_NN_GeomSmooth?_SO
18 Mar 2015, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Node depths were being computed along the principal direction closest to Z
The proper intent is along the principal direction, regardless of
whether or not it is closest to the Z direction
12 Mar 2015, RC Reynolds, afni_base.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed capture in shell_exec2 for old python, where readlines() would hang
03 Mar 2015, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed misuse of strncat in distribution
03 Mar 2015, RC Reynolds, powell_int.c, level 1 (MICRO), type 4 (BUG_FIX)
multiple include directives got joined on one line
02 Mar 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed 3dTproject call for resting state on surface
Thanks to Tara (message board) for noting the problem.
26 Feb 2015, DR Glen, align_epi_anat.py align_centers bug, level 2 (MINOR), type 4 (BUG_FIX)
align_centers always called by mistake
25 Feb 2015, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Patched ID collisions for input datasets
23 Feb 2015, ZS Saad, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
Patched source for hash collisions on file names
19 Feb 2015, DR Glen, @Align_Centers child bug, level 2 (MINOR), type 4 (BUG_FIX)
child datasets not created properly
If creating new shift datasets (the default), the
datasets would not be properly updated to reflect
the new origin shift.
26 Jan 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Hadn't included part quantitative interaction term in qVars list.
Program wouldn't run if interaction term had quant var.
23 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Rare scenario of -nifti -dump_rois AFNI not working.
Needed to add a mkdir() internally. Itsafinenow.
22 Jan 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed some issues when only a tiny number of voxels is in inset.
Labelling wasn't correct when nvox < n_refset_roi.
21 Jan 2015, ZS Saad, 3dSkullStrip, level 1 (MICRO), type 4 (BUG_FIX)
Made program take sub-brick selectors at input.
Involved bringing SUMA_AfniExists() and SUMA_AfniPrefix() from stone age.
15 Jan 2015, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed () in case of r(A,B,unbiased=1), which matches correlation_p()
15 Jan 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
include -demean when running 3ddot on masks
08 Jan 2015, DR Glen, @Shift_Volume, level 1 (MICRO), type 4 (BUG_FIX)
No need to update space for simple shift option
Previous version reported error for RAI shift but produced correct results
10 Dec 2014, RC Reynolds, meica.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed 3dTshift input in case of --no_despike
Thanks to M Plitt for the code fix.
09 Dec 2014, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Make 'Alpha' mode work with Montages -- oops
There's probably other stuff that doesn't work with RGBA overlays, but
we'll have to see what happens.
05 Dec 2014, RW Cox, 3dNwarpApply, level 3 (MAJOR), type 4 (BUG_FIX)
Forgot to index-ize the matrix warps before applying them!
In the revised way of catenating time-dependent warps, the matrix warps
are kept in xyz coords until they are actually used, when they should be
transformed to ijk coords. In the 'old' way, they were transformed
directly on input. But in the 'new' way, I forgot to transform them
before applying them in the catenation loop, and the results were not
pretty. I'm still searching for someone to blame for this, since it
clearly can't be MY fault. Any volunteers?
04 Dec 2014, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Default coloring of directions was using negative values.
No so good for openGL colors. Negative values get clamped at 0.
Default coloring is now ABS(X|Y|Z) now.
02 Dec 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
added floatscan to THD_load_nifti for case of double->float conversion
Thanks to M Gregory.
02 Dec 2014, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
-tlrc_NL_awpy_rm was not being applied
02 Dec 2014, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
fixes for child_anat and mean epi base
Thanks to Isaac Schwabacher for the child_anat fix!
02 Dec 2014, DR Glen, @Align_Centers, level 1 (MICRO), type 4 (BUG_FIX)
fix for 1Dmat_only output
Datasets were output or modified even with this option,
Now just the transformation matrix is output
24 Nov 2014, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 4 (BUG_FIX)
Fixed floating point precision error that resulted in error message
19 Nov 2014, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
do not allow num_suffix to be processed as octal
07 Nov 2014, RC Reynolds, mri_nwarp.c, level 1 (MICRO), type 4 (BUG_FIX)
applied update to free temporary warp on behalf of RWC
27 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed strcmp trap in -sbns; have -sb_num_suffix look for any last integer
24 Oct 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Fixed offset in track to volume coordinates
Effect of bug restricted to viewing of tracts rather than volume masks and
connectivity matrices.
Offset was by half a voxel in each of the three dims.
23 Oct 2014, RW Cox, 3dNwarpCat, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug introduced with changes made for 3dNwarpApply
22 Oct 2014, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 4 (BUG_FIX)
if padding for dilate/erode steps, preserve ijk_to_dicom_real
Thanks to A Kurani for noting the problem.
20 Oct 2014, RC Reynolds, imcat, level 2 (MINOR), type 4 (BUG_FIX)
z and r: fixed y-padding
08 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
added -save_errors and more recovery chances, fixed sb_num_suffix app
Stage 3 of sorting broke stage 2 of sorting.
Thanks to V Roopchansingh for noting the problem.
30 Sep 2014, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug with NUMLOCK keeping surfaces from rotating on linux!
25 Sep 2014, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
fixed use of altered add_to_string_list()
The changed usage broke options -drive_afni, -drive_wait and -rt_cmd.
Thanks to V Roopchansingh for noting the problem.
24 Sep 2014, ZS Saad, ConvertSurface, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug with line projection of coordinates.
23 Sep 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
cat_strings was missing trailing byte
Thanks to Q Li for noting the problem.
22 Sep 2014, RC Reynolds, column_cat, level 2 (MINOR), type 4 (BUG_FIX)
fixed implementation of -line, which messed up default operation
17 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
A few miscellaneous errors here and there
One was caused by extra space in driver command
Another was caused by loading multiple surfs on the command line
followed by a command line drive command.
Intersection parameters were not fully initialized under some conditions.
17 Sep 2014, DR Glen, auto_warp.py, level 1 (MICRO), type 4 (BUG_FIX)
Did not pass qw_opts properly to 3dQwarp
16 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Use of percentiles in range settings was broken. That is no more.
Problem was caused by reliance on colp->V without resetting it
when a new range was set. That is because colp->V gets clamped
by the range of values being set.
12 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Crosshair mismatch when prying surfs in multiple linked viewers
12 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash caused by toggling off 'I' selection for volumes
08 Sep 2014, RC Reynolds, plug_realtime, level 1 (MICRO), type 4 (BUG_FIX)
fixed free_PCOR_ivoxel_corr function call typos
Thanks to Y Halchenko for noting the problem.
08 Sep 2014, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
num_chan > 1 needs 3D+t ACQ type
Thanks to V Roopchansingh for noting the problem.
03 Sep 2014, ZS Saad, 3dSetupGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Made -labels option work well with -LRpairs
03 Sep 2014, RW Cox, sorting, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug in special qsort7_* code -- had wrong indexes!
Affects any program calling qsort_float() for array of length 7
03 Sep 2014, RW Cox, r_idisp.c, level 1 (MICRO), type 4 (BUG_FIX)
Fixed formatting bugs (%ld changed to %lld) in 2 places
02 Sep 2014, RW Cox, 3dNwarpAdjust, level 1 (MICRO), type 4 (BUG_FIX)
Tried to write out average dataset when it didn't exist -- Oops.
Also fixed bug in mri_nwarp.c where extended warp dataset didn't get the
same 'view' as the input dataset.
25 Aug 2014, ZS Saad, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
Made program handle NIFTI input. Irrrrgh.
25 Aug 2014, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 4 (BUG_FIX)
defined oind (for case that does not currently happen)
11 Aug 2014, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug with -pblur
Problem: warped source image Haasrcim was created from source image
blurred at lev=0, which means (with -pblur) it was blurred a lot. Then
at later levels, it is being slowly replaced with warped patches from a
less-blurred source image. This produces strange effects, as part of
Haasrcim is now heavily blurred and part is less blurred. Solution:
re-create Haasrcim from the current warp and from the current amount of
blurring at the start of each level.
11 Jul 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed 1d_tool.py -pad_into_many_runs for bpass w/varying run lengths
Thanks to d6anders for noting the problem.
03 Jul 2014, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
pbar locks didn't work right all the time
Needed to force things to happen more violently, and also to force
overlay redraws. Also, make a new controller be locked at startup
instead of when the user does something.
03 Jul 2014, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
'u' keypress failed when OLay and ULay datasets were the same
Toggling between overlay and underlay as grayscale with 'u' failed when
the 2 datasets were the same. Problem devolved to a function Ziad put
in to make the selection of sub-brick index to use -- which always
favored the anat_index if the 2 datasets were the same, regardless of
the image type requested. Now it should work properly -- when the 2
datasets are the same (fim and anat), then the sub-brick index will be
chosen based on the type of image requested.
03 Jul 2014, RC Reynolds, model_conv_PRF, level 2 (MINOR), type 4 (BUG_FIX)
fixed a name space problem on macs
03 Jul 2014, DR Glen, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
oblique NIFTI dataset handling
NIFTI datasets with oblique orientations were written
with incorrect (original) orientations after alignment. Dataset is
now cardinalized and input obliquity is ignored
25 Jun 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
removed SUMA/SUMA_MakeColorMap, SUMA/SUMA_MakeConsistent from source tree
Thanks to Y Halchenko for bringing it up.
10 Jun 2014, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Fix crashing bug with PBAR_FULLRANGE
b..._ulay pointers could become deranged via AFNI_setup_viewing() call
to AFNI_reset_func_range() -- patched this, and also check for this type
of derangement in various other places -- ERROR_message should appear if
it raises its ugly head again.
06 Jun 2014, P Taylor, 3dEigsToDT, level 1 (MICRO), type 4 (BUG_FIX)
Make help file option match with actual usage.
Fixed a minor mismatch of helpfile name and actual option name.
23 May 2014, DR Glen, whereami linkrbrain, level 2 (MINOR), type 4 (BUG_FIX)
Fixed linkrbrain coordinates and malloc/free error
Coordinates were not transformed properly from TLRC to MNI
space. Crashes from clusterize in afni GUI caused by mismatched
AFNI-friendly malloc, free in strdup function
19 May 2014, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
NIFTI dataset input and save_skullstrip
Fixed bug with both NIFTI input and save_skullstrip
16 May 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
make space in case compression programs have longer paths
Thanks to D Thompson for finding the problematic code.
12 May 2014, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
-part_init 0 is not appropriate for -partition
Text labels now apply, and the default is '-part_init INIT'.
01 May 2014, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
added -quick option; fixed recursive backups
24 Apr 2014, RC Reynolds, afni_history, level 1 (MICRO), type 4 (BUG_FIX)
added proto for restrict_hlist()
18 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Color map changes/thresholding changes now working with multi-viewers
This was not the case before. Problem was that Texture had to be reloaded
for all viewers displaying the volume, once the viewer's rendering context
is current. That's all handled via per_sv_extra[]
16 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with opening new controllers when cont. window is closed
See Apr. 16 2014 note in function SUMA_viewSurfaceCont()
16 Apr 2014, P Taylor, 3dMatch, level 2 (MINOR), type 4 (BUG_FIX)
Bug when using mask on *some* files with Linux.
Seems to be more stable criteria now.
16 Apr 2014, P Taylor, 3dROIMaker, level 1 (MICRO), type 4 (BUG_FIX)
Hadn't made a problem if user didn't input 'prefix'.
Fixed aforementioned loophole..
10 Apr 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
@afni.run.me never made it into Makefile.INCLUDE for distribution
04 Apr 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed reading NIFTI obliquity w/dglen (lost Mar 22)
Thanks to P Kundu for noting the problem.
27 Mar 2014, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
h_view help added
26 Mar 2014, RC Reynolds, auto_warp.py, level 2 (MINOR), type 4 (BUG_FIX)
in 3dNwarpApply, use the base dataset as the -master, rather than WARP
The WARP dataset is now often bigger, to handle warps to the dataset
edges. The result from auto_warp.py should match the template/base.
Note: the problem applies to binaries from 3/21 until 3/25 (now).
Thanks to V Zachariou for noting the problem.
21 Mar 2014, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
problem with zeropadding plus -iniwarp
Zeropad produces a warp that is bigger than the dataset. That's OK
(even in 3dNwarpApply), but 3dQwarp would cut it off when writing it
out. That's still OK for 3dNwarpApply, but NOT OK for re-start with
-iniwarp -- the zeropadded initial warp will have a discontinuity at the
edge of the volume, and that's bad. The fix is to allow input of the
initial warp to be either at the dataset size OR at the zeropadded size.
Also add the -pencut option, to give finer control over the penalty.
This needs some experimentation.
21 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if anaticor and censor, do not use keep_trs for blur est from errts
Thanks to J Stoddard for noting the problem.
21 Mar 2014, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
removed -e from 'tcsh -ef @ss_review_basic', for grep failures
Macs terminate (correctly) when grep/wc return non-zero status, but
Linux systems do not. Maybe tcsh authors did not like grep killing
scripts, either...
20 Mar 2014, RC Reynolds, 1dUpsample, level 2 (MINOR), type 4 (BUG_FIX)
fix reporting of file name in error messages; enhance said messages
18 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Improved selection logic on slices and for graphs.
Graph selection was changed so that what is rendered is selectable.
The alternate was too confusing.
Fixed bug with selections on matrix where selections at times were
going to the volume, even though it is not displayed with the matrix.
Fixed slice highlighting when in montage mode.
Added alpha value threshold condition to slice picking. This slows the
selection process a little, but it keeps one from selecting 'air' when
when clicking on voxels that meet the threshold but are alpha masked.
17 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed residual surface shading after volume is selected.
Problem was caused by residual emissivitiy colored left over
from the highlighting of the selected slice. Also wrote functions
SUMA_DiffEnablingState*() to help identify such problems.
13 Mar 2014, RW Cox, fdrval, level 1 (MICRO), type 4 (BUG_FIX)
two changes
(a) bug fix in interp_inverse_floatvec(), where the last interval wasn't
used -- in the context of fdrval, tiny qval (big zval at end of range)
would be missed, giving bogus output
(b) alteration in THD_fdrcurve_zqtot(), where if the input zval is past
the end of the range, then the largest value in the threshold sub-brick
is returned if it is bigger than the value returned by
interp_inverse_floatvec()
13 Mar 2014, RW Cox, AFNI, level 1 (MICRO), type 4 (BUG_FIX)
Didn't properly turn off dplot in Boxed graphing mode
12 Mar 2014, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
SUMA crashed if you deleted a tract mask that was being moved.
This is now a thing of the past.
10 Mar 2014, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Fix memory handling errors
(1) when loading a NIfTI dataset, it should be unloaded first to avoid
memory leakage
(2) when creating a vectim from a censored list, the correct check is if
the subset is NOT loaded -- the test was backwards :-(
06 Mar 2014, P Taylor, 3dDWUncert, level 2 (MINOR), type 4 (BUG_FIX)
Silly bug-- order of options not free.
Changed how options were processed so they weren't order-dependent.
06 Mar 2014, P Taylor, 3dROIMaker, level 1 (MICRO), type 4 (BUG_FIX)
Make parameter appear in help file correctly.
Fixed silly Spoonerism in option names usage/help-representation.
05 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Opening surf controller after selecting voxel on slice caused crash in demo
This happened in FATCAT_DEMO's Do_09* script, example 1 (SET1). While I am
still unsure what caused the Bad Window error, I now trap for it and keep
the program from getting shutdown. Some day I'll track the source of the
message, for now, recovery seems complete.
04 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Surface-based InstaCorr stopped refreshing with new click.
The problem was caused by the failure to update the copies of I and
T columns in the overlay structure when a new dataset replaced an older
version. For the fix, search for 'ResetOverlay_Vecs' string, and see
function SUMA_DSET_ClearOverlay_Vecs()
25 Feb 2014, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Modified Makefile.macosx* to start building SurfMesh again.
20 Feb 2014, RC Reynolds, 3dClustSim, level 1 (MICRO), type 4 (BUG_FIX)
break WARNING_message(amesg) up, until W_m gets enhanced
Strings applied via the format are limited to 16K.
19 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash during crazy matrix rotations.
The problem was caused by divisions by very small sizes under certain
projection (viewing) angles
19 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed indexing errors in sparse matrices with certain node (point) lists.
The problem occurred when point lists were supersets of the points used to
define the edges.
19 Feb 2014, ZS Saad, ConvertDset, level 1 (MICRO), type 4 (BUG_FIX)
Removed stringent test on number of points in edge list
The program insisted on having the same number or points (nodes)
in the node list as there are unique points making up the graph.
19 Feb 2014, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX)
Some of the pbar 'flip' controls didn't redraw the overlay
Also, scroll wheel in the pbar label (atop the color bar) will now do
the flipping as well.
19 Feb 2014, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
if AM2 or IM, terminate extraction of ideals
Ideal extraction should be done via 1d_tool.py, using the X-matrix.
17 Feb 2014, DR Glen, @MakeLabelTable, level 1 (MICRO), type 4 (BUG_FIX)
-centers option incorrect for some atlases
incorrect centers of mass for datasets with missing ROI values
07 Feb 2014, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with -allineate option
3dAllineate might choose to write out a .nii.gz file instead of the .nii
file ordered. In that case, 3dQwarp fails to read it in. The fix -- if
the .nii file doesn't exist, then add '.gz' to the end of the filename
and try again, before giving up and going home to mother.
31 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with graph where segments were turning black.
Problem was caused by a stale pointer copy stored in SDO->colv
bad bad bad!
15 Jan 2014, RC Reynolds, 3dLRflip, level 1 (MICRO), type 4 (BUG_FIX)
used bad filename without -prefix
Var ext was not initialized.
09 Jan 2014, DR Glen, 3dDWItoDT, level 2 (MINOR), type 4 (BUG_FIX)
bmatrix options
bmatrix_Z and bmatrix_NZ options replace old -bmatrix option
The new options allow for a B=0 and no B=0 row in an optional
b-matrix input. The b-matrix may be used as input instead of the
gradient vector direction file. The former -bmatrix option
resulted in an error or incorrect results. (Paul Taylor is mostly
responsible for recognizing and fixing this. Thanks, Paul!)
08 Jan 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem introduced by earlier -graph_named_nodelist_txt change
Problem was one of parsing and made the program fail to read in all
entries in labels file.
30 Dec 2013, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
madd initial NT parametercw_malloc.c: moved mcw_malloc_dump_sort below _dump for solaris
Apparently it does not like inconsistent declaration in same file,
and mcw_malloc.h does not offer prototypes to many functions in the
case of DONT_USE_MCW_MALLOC, including this one.
24 Dec 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed SUMA's erroneous switch of colplanes for tracts
Problem was in thoughtless use of SUMA_ADO_Overlay0() instead
of available curColPlane pointer in SUMA_cb_createSurfaceCont_TDO().
Similar changes were made to other SUMA_cb_createSurfaceCont_*() functions
where curColPlane must be non null at the time of controller creation.
22 Dec 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed problem with graph edge selection when viewing connections from node
Problem is mismatch between colid and what gets rendered when it is not
the whole object being displayed. For now, everything BUT thresholded
edges will get rendered during selection, regardless of what is being
displayed
17 Dec 2013, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
SUMA stopped building on systems lacking glCheckFramebufferStatus()
That was basically all linux_* systems since they are quite a few
versions behind. The patch is activated with a define at make time.
Set SUMA_MDEFS = -DSUMA_GL_NO_CHECK_FRAME_BUFFER in Makefile.* if
the OpenGL installed does not support glCheckFramebufferStatus().
Note that -DSUMA_GL_NO_CHECK_FRAME_BUFFER is not really needed for
most build machines because the code uses other ways to check for
glCheckFramebufferStatus(). However these auto checks failed on
hurin so SUMA_GL_NO_CHECK_FRAME_BUFFER is still necessary for the moment
17 Dec 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed SUMA's opacity cycling with 'o'
NULL
16 Dec 2013, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed use of num_trs in the case of censoring
Thanks to K Kerr for noting the problem.
10 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed source of undefined buffer and problem with glXMakeCurrent on OS X
Problem seems caused by attempting to create an X graphics context when
creating a new suma viewer. XCreateGC is no longer needed - its context
has not been used for a long while anyway.
09 Dec 2013, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed broken demo script run_stdmesh_demo from std_meshes.tgz
Failure was in glXMakeCurrent which crashed rather than return in error.
Not sure what was causing this, but it was the rapid succession of
controllers being open and repositioned that was causing this. Simply
splitting the two operations into separate loops was enough to remedy
this. Adding calls to glFinish() and XSync() did nothing to fix the
problem reliably
09 Dec 2013, RC Reynolds, afni_util.py, level 2 (MINOR), type 4 (BUG_FIX)
added backup function for get_process_stack
BASE.shell_com() might return a short process list, probably from
limited buffer space (for cmd.stdout).
04 Dec 2013, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
fixed ac++ condition and empty if
05 Nov 2013, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
watch out of 'afni -ver' crashing because of missing libraries
Trap check of $package, since it is included with $status.
Thanks to CC Yen for noting the error.
28 Oct 2013, P Taylor, 3dMatch, level 2 (MINOR), type 4 (BUG_FIX)
Fixed subbrick labelling oddity.
For some reason, subbrick selection with [i] was getting confusedwith i-th
label (which was an integer). Solved by prefixing labeldesignation with a
short string of useful letters.
24 Oct 2013, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fix segmentation error when not using -refset.
Fixed error in defining/freeing a certain array.
22 Oct 2013, RW Cox, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Found that -noline didn't work right with 2 or more time series!
17 Oct 2013, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
avoid infinite loop on empty SYM: or SYM: rows
26 Sep 2013, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
added more .h files to install_lib for compiling outside of afni_src
Added rcmat.h, misc_math.h, thd_atlas.h, thd_ttatlas_query.h
and thd_ttatlas_CA_EZ.h.
20 Sep 2013, RW Cox, ccalc, level 1 (MICRO), type 4 (BUG_FIX)
Fixed Ziad's stupid sprintf(buf, ... , buf) bug
17 Sep 2013, RW Cox, afni_driver.c, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with SET_PBAR_ALL +99
Didn't properly enforce the positivity.
13 Sep 2013, RC Reynolds, 3dNLfim, level 1 (MICRO), type 4 (BUG_FIX)
report an error instead of crashing if no -input is given
This allows for getting individual signal help without the crash.
05 Sep 2013, ZS Saad, 3dSeg, level 1 (MICRO), type 4 (BUG_FIX)
Fixed crash happening after write operation in 3dSeg
The problem happened when a dataset is written with a byte
order that differs from the original one. Under this scenario
the dataset gets purged from memory by the writing function.
Kudos to Isaac Schwabacher for doggedly pursuing the bug.
03 Sep 2013, ZS Saad, MapIcosahedron, level 1 (MICRO), type 4 (BUG_FIX)
Program was crashing with message about binSearch failing.
Problem was caused by recent changes to binSearch that forced
exact matching.
03 Sep 2013, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
Dimon -rt: if im_is_volume and single volume, get dz from image
Thanks to A Nilsen for reporting the problem.
26 Aug 2013, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Program crashes or gets bad answers on very large datasets
Problem: with a vectim, the pointer to the k-th voxel time series array
(of length nvals) is calculated as
ptr = base + k * nvals
where k and nvals are ints. But with gcc, the k*nvals value is then
computed in 32 bit arithmetic before being added to the 64 bit pointer
'base'. Not good when you pass the 2,147,483,647-th voxel -- that is,
if the vectim is over 8 Gbytes. With the Intel icc, it apparently works
OK -- bravo for Intel. Anyhoo, by casting k and nvals to size_t, this
problem goes away. For now.
26 Aug 2013, P Taylor, DoTrackit.c, level 2 (MINOR), type 4 (BUG_FIX)
Fix handling of non-RPI datasets.
No ostensible output change, except to not produce an error message.
21 Aug 2013, P Taylor, 3dRSFC, level 2 (MINOR), type 4 (BUG_FIX)
Allow subset of time series to be selected.
Minor tweaking of internal workings for writing output.
No quantitative change.
15 Aug 2013, RW Cox, cs_symeig, level 1 (MICRO), type 4 (BUG_FIX)
Modify backup for svd_double failure
gcc-compiled source for eispack SVD function sometimes gives wrong
results. The backup code for this also sometimes fails. So I modified
the backup in 2 ways -- perturb the matrix by a factor of 1e-13, and if
that fails, call a second backup SVD function. Sheesh.
02 Aug 2013, RC Reynolds, 3dANOVA, level 2 (MINOR), type 4 (BUG_FIX)
if AFNI_COMPRESSOR and input nii.gz, 'remove()' would not remove BRIK.gz
Thanks to P Molfese for noting the problem.
01 Aug 2013, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
in suma_gifti.c, convert GIFTI's LPI to and from AFNI's RAI
Done with Ziad. Thanks to N Oosterhof for bringing this up.
01 Aug 2013, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fixed apparent pointer step issue, which happens on only some systems
Apparent problem with MMAP (memory mapping of files).
Thanks to W Gaggl for pointing out the problem.
31 Jul 2013, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fixed failure to apply a negative dilation in non-convert case
Thanks to W Gaggl for noting the problematic scenario.
29 Jul 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Coordinates xform of GIFTI surfaces was applied too late
18 Jul 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
Yet another indexing error (in argv[], no less)
17 Jul 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
fixed indexing error in duplo_up for odd-sized grids
17 Jul 2013, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
fixed problem with -zclip in the source volume - indexing error
06 Jul 2013, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
use NIFTI_INTENT_NONE for case of intent_code = FUNC_BUCK_TYPE
3dbucket's FUNC_BUCK_TYPE went to intent_code for 1 vol dset
13 Jun 2013, RW Cox, 3dLocalHistog, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug that caused first value from label table to be lost
Or actually, subsumed into the 0=Other histogram. stupid stupid stupid
14 May 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Renamed motion files for -save_vr without -epi2anat
13 May 2013, RC Reynolds, @RenamePanga, level 2 (MINOR), type 4 (BUG_FIX)
added -column to count commands writing listfile
There is a 4096 byte limit in addto_args(), which could be made dynamic.
10 May 2013, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
named glob functions as afni_*; R was using sys funcs, rather than local
09 May 2013, ZS Saad, R_io, level 2 (MINOR), type 4 (BUG_FIX)
Temporary fix of segfault happening in R from R_io.so
Source of problem is a call to COMPRESS_setup_programs()
Not sure why the following crash was happening:
*** caught segfault ***
address 0x3800000100, cause 'memory not mapped'
However a temporary env. SKIP_COMPRESS_SETUP will get around it.
24 Apr 2013, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 4 (BUG_FIX)
did not set 'ver' before goto START
Thanks to I Schwabacher for noting the problem and fix.
24 Apr 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX)
allow -space for nifti; actually exit if -view and result exists
Thanks to I Schwabacher for noting the problem and fix.
18 Apr 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX)
-useweight didn't actually do anything inside OpenMP
Obviously, this can't be my fault. I blame evil spirits.
17 Apr 2013, RC Reynolds, 3dAFNItoNIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed old use of use of strcat() after strdup()
Thanks to B Benson and J Stoddard for noting the problem.
17 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_vr result causes crash
16 Apr 2013, RC Reynolds, 3dmaxima, level 2 (MINOR), type 4 (BUG_FIX)
modernize dataset coordinate reporting, using proper signs
Thanks to G Pagnoni for reporting the issue.
15 Apr 2013, RC Reynolds, 3dSurf2Vol, level 1 (MICRO), type 4 (BUG_FIX)
fixed crash when a surface was not found (struct init)
Thanks to H Yang for noting the problem.
09 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed computed fitts for REML case (was from 3dDeconvolve)
Thanks to G Pagnoni for noting the problem.
01 Apr 2013, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
AFNIio.R's newid.AFNI() was duplicated and the more compact one was broken
01 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Some output files like the motion files were accidentally renamed.
28 Mar 2013, ZS Saad, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX)
Parsing of -on* and -off* options failed for non-integral values
26 Mar 2013, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Loop variable error in 3DEdge/src/convert.c variable s32buf
Affected regions in some locations under: case UCHAR and case SSHORT
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Texture demos in DriveSuma were failing.
Problem was a combination of coordinate clipping when frame coords
were at 0 or 1. That is now fixed. Also, demo.*do files needed changing
to move texture on surface into mobile.niml.do
Depth test is no longer disabled with textures.
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Text was not appearing at times. Bug was in SUMA_SO_NIDO_Node_Texture()
19 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Prying was off for new GIFTI standard-mesh surfaces.
Bug was caused by a failure to identify LR sides of GIFTI
surfaces. SUMA was not preserving the side of a GIFTI surface
at write time in SUMA_GIFTI_Write(). Code was also modified
to guess the side of pre-existing GIFTI surfaces.
Prying was also off when a transform was found in the header
of the surface volume because dimensions were not being recomputed
after applying the VolPar transform. That is now fixed.
19 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
alignment AddEdge error
Error in resampling step of AddEdge procedure causes crash.
Problem requires both -giant_move (or -prep_off or -resample off) and
-AddEdge.
14 Mar 2013, P Taylor, 3dDWUncert, level 2 (MINOR), type 4 (BUG_FIX)
Silly bug in e_{13}^* estimation.
Mean and std of uncertainty of e1 toward e3 was buggy.
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed FOV problems for auto setting and fixing zoom level across states
22 Feb 2013, P Taylor, rsfc, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential float/double problem.
When using 3dReHo to get ReHo for ROIs, could get *very* large numbers
during part of calculations; floats were fine for 27 voxel neighborhood,
but not with large ROIs. Thus, using doubles in the calc now.
22 Feb 2013, P Taylor, 3dReHo, level 1 (MICRO), type 4 (BUG_FIX)
Fixed mask misread which could cause error in some nonmasked data.
22 Feb 2013, P Taylor, 3dDWUncert, level 1 (MICRO), type 4 (BUG_FIX)
Free as well as DELETE a dset.
Ultraminor change.
14 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
handle surface data in -move_preproc_files
Thanks to P Molfese for reporting the error.
12 Feb 2013, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
updated duplicate dataset error message to match older code updates
Thanks to HJ Jo for reporting the error.
12 Feb 2013, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
if 'afni -ver' fails from libraries and $status not set, check $package
06 Feb 2013, P Taylor, 3dTrackID, level 1 (MICRO), type 4 (BUG_FIX)
Small bug in 3dTrackID fixed.
In post-run freeing of variables, had been error for a char string.
06 Feb 2013, P Taylor, 3dRSFC, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential div by zero in 3dRSFC.
05 Feb 2013, RC Reynolds, python-general, level 1 (MICRO), type 4 (BUG_FIX)
fixed (unused) cols_by_label_list functions
Fix by I Schwabacher, who is actually using the function.
04 Feb 2013, ZS Saad, R, level 1 (MICRO), type 4 (BUG_FIX)
Properly set IDCODE of new dsets, read .1D.dset as dset not matrix
31 Jan 2013, RC Reynolds, uber_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed blist error that had not been converted to bdict
Thanks to Piero C. for reporting the error.
18 Jan 2013, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
when jobs=1, only warn for -virtvec if the option was used
The result was just a warning which did not affect processing.
Thanks to J Britton and E Ronkin for reporting the warning.
04 Jan 2013, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would make 3drefit exit if dataset contains a warpdrive attribute
02 Jan 2013, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
in THD_cmass(), if mask is NOT set, clear data value
Found with dglen. This is an old bug, ick.
31 Dec 2012, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
is_in_labels(): search for longest match
To fix failure in the case of both label and labelSUFFIX existing.
28 Dec 2012, RC Reynolds, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
mri_polyfit() now takes exar parameter, pass NULL
27 Dec 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Increased buffer size for reading one line.
See LBUF in mri_read.c, also added error message when
line is too long for LBUF in afni_fgets()
21 Dec 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
change check for recur download by looking for known string in script
Thanks to S Lowell for reporting the error.
20 Dec 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 4 (BUG_FIX)
remove -volreg_tlrc_warp in case of no tlrc block
Thanks to P Taylor for reporting the error.
18 Dec 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
have THD_subbrick_minmax fall back to THD_slow_minmax_dset if no STAT
This is a fix for 3dSkullStrip on NIfTI dsets.
Thanks to kelvin for reporting the error.
15 Nov 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Guarded against NULL strings in THD_dblkatr_from_niml()
These strings came via R_io.c, but could come from elsewhere.
14 Nov 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed check for random space in -max_consec case
Thanks to Kristina for reporting the error.
13 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed fopen_maybe to check for .1D suffix on file streams
Suffix might get added by EDIT_dset_items.
Thanks to I Schwabacher for reporting the error.
09 Nov 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash on OSX 10.7_64 apparently caused by gcc's optimization
The fix entailed adding -O1 to target SUMA_xColBar.o in SUMA's
SUMA_Makefile_NoDev. I also changed the way SurfaceControllers
are put away. They are now minimized thus keeping the widgets
realized.
01 Nov 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed problem with very large threshold ranges
X11 scale cannot range more than MAX_INT/2. SUMA nowchecks for that and wa
rns the user.
23 Oct 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
forgot to leave show_size_n_offset set
Thanks to J Jarcho for reporting the to3d failure.
18 Oct 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 4 (BUG_FIX)
small updates to correspond with library changes
16 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed functions that generate volume masks from surfaces
There was a bug in SUMA_FindVoxelsInSurface() and SUMA_SurfGridIntersect()
which made for ugly masks in the fast mode. This is no longer the case,
SUMA_FindVoxelsInSurface() is about as good as its sister function
SUMA_FindVoxelsInSurface_SLOW(), but considerably faster.
This bug fix might affect some 3dSkullStrip and 3dSurfMask results. The
more voxel sizes differ from 1x1x1, the more noticeable the difference
might be.
16 Oct 2012, DR Glen, afni show atlas colors, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would crash afni if paned color and show atlas colors
15 Oct 2012, RW Cox, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug with -CENSORTR run wildcards and coloring
15 Oct 2012, RW Cox, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug with 'push' and '-yaxis' interacting badly.
12 Oct 2012, ZS Saad, 3dedge3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed scaling problem for short/byte data.
12 Oct 2012, RC Reynolds, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX)
set AEA_opt in quotes, as it might be a list
04 Oct 2012, ZS Saad, MapIcosahedron, level 1 (MICRO), type 4 (BUG_FIX)
Dset Mapping failed on sparse datasets, at times.
26 Sep 2012, RC Reynolds, nifti_tool, level 2 (MINOR), type 4 (BUG_FIX)
changed ana originator field from char to short
25 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use errts_REML to compute blur if 3dD_stop; apply compute_fitts if no reml
Thanks to P Molfese for reporting the problem.
22 Sep 2012, ZS Saad, 3dkmeans, level 1 (MICRO), type 4 (BUG_FIX)
Fixed default prefix which was overwriting input.
Also added default selection when input has single value
12 Sep 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Stupid null character termination missing in THD_filepath()
12 Sep 2012, ZS Saad, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Fixed incorrect warning in 3dttest++ about labels and filenames
The warning is intended to be sure users don't mess up the
-setA option when using the long form. The warning message
was being triggered incorrectly, this should no longer be the case.
Warning did not affect results.
11 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed 'potential' crash in SUMA_SetScaleThr_one()
11 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed potential corruption in macro SUMA_NEL_REPLACE_STRING
Not sure to make of this problem, but bad reads/writes
are happening in m_rc[(row)] in the macro, and to cs[n0++]
in cs[n0++] = lbl[i]; of SUMA_AddColAtt_CompString(). In fact
the first problem happens in cs[n0++], so the problem might
start there. In any case, the fix was to increase the length
of allocated segment by +10 instead of +1 in SUMA_NEL_REPLACE_STRING
That seems to do the trick.
10 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Typing in sub-brick arrow fields was ignored on linux
Problem due to incorrect error checking from strtod()
06 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
SUMA's sub-brick arrowfields were not updating properly
04 Sep 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed error message in case of different group sizes
Error pointed out by Priyank.
29 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI build was failing on machines where DONT_USE_MCW_MALLOC was defined
The cause of failure was a missing #define NI_calloc() when
DONT_USE_MCW_MALLOC is defined. The one line needed is now in niml.h.
Builds likely affected are solaris and macosx_10.7_Intel_64
Affected build dates from about Aug. 24th to Aug. 29th.
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed interaction with L/R yoking asynchrony.
Problems included interaction with clustering setting and with
Intensity/Threshold/Brightness selectors.
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed some L/R yoking problems and a crash source in drive mode.
The crash was caused when calling SUMA_Set_Menu_Widget() on a controller
not fully realized.
24 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed SUMA<-->AFNI cross hair linkage with multiple anat. correct surfaces
It used to be that a coordinate always got attached to the Local Domain
Parent surface. Even if you clicked closest to a node on the Pial surface
SUMA would jump to the corresponding node on the smoothwm surface. This wa
s
way uncool.
24 Aug 2012, ZS Saad, @ScaleVolume, level 1 (MICRO), type 4 (BUG_FIX)
step(a) was used instead of bool(a) for masking operations
This caused zeros in the output where input values were negative.
Also added a modifier to the labels to highlight that features were
scaled.
17 Aug 2012, RC Reynolds, 3dGroupInCorr, level 1 (MICRO), type 4 (BUG_FIX)
pass 'batch mode' var to SUMA_init_GISET_setup to preserve dset
15 Aug 2012, DR Glen, whereami web, level 1 (MICRO), type 4 (BUG_FIX)
Web-based atlases would not open webpage with ampersands, punctuation
14 Aug 2012, DR Glen, 3drefit -epan error, level 2 (MINOR), type 4 (BUG_FIX)
Removed error for refitting data type
3drefit would exit with error for -epan and multi-subbrick data
Removed incorrect checks against archaic timepoints per TR nvals
09 Aug 2012, RC Reynolds, afni_general, level 1 (MICRO), type 4 (BUG_FIX)
definition after ENTRY in mri_genalign_util.c
08 Aug 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 4 (BUG_FIX)
currently need to pass -sv even for -on_surface; get rid of this later
08 Aug 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
do not update tlrc anat with strip if passed in
31 Jul 2012, RC Reynolds, 3dresample, level 2 (MINOR), type 4 (BUG_FIX)
update IJK_TO_DICOM and _REAL at end of resample library function
Thanks to I Schwabacher for reporting the IJK_TO_DICOM discrepancy.
26 Jul 2012, RC Reynolds, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
K text columns (after label) would result in K lost float columns
Thanks to Phoebe of Harvard for reporting the problem.
10 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made default prefix path be ./ instead of path of input
The change was done to function EDIT_empty_copy() which assigned
to a pathless prefix the path of the input dataset if the latter
was specified. The problem was that something like:
3dMean -prefix mmm P1/joe+orig P2/jane+orig
would have written mmm+orig under P1/
To make matters less palatable other programs like 3dcalc behaved
differently: 3dcalc -prefix ccc -a P1/joe+orig -expr 'a'
would produce ./ccc+orig
28 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed help error regarding IM
Thanks to I Blair for reporting it.
28 Jun 2012, DR Glen, Draw Dataset plugin, level 2 (MINOR), type 4 (BUG_FIX)
Resampling of atlas regions to lower resolution undercounted
Draw Dataset plugin atlas resampling to a lower resolution dataset
undercounts number of voxels. Incorrect usage of temporary volume
in byte storage was fixed with float volume. Additionally, new
environment variable, AFNI_DRAW_THRESH, allows for variable
threshold level (done with RCR)
25 Jun 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed uninitialized cpad1,2 in the case of no censoring
20 Jun 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 4 (BUG_FIX)
comment out plot_ts_setthik() type calls for now
When registering, finalize_dset() will result in white image window.
Thanks to V Roopchansingh for reporting the problem.
19 Jun 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Ctrl+W was not saving datasets when filenames contained a path
Problem had to do with clumsy prefix forming.
14 Jun 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
use afni -com instead of plugout_drive (for case of multiple users)
Thanks to V Razdan and N Adleman for reporting the issue.
06 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
look for input of EPI datasets in standard space and NIfTI format
05 Jun 2012, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 4 (BUG_FIX)
need to explicitly set DSET_BRICK_TYPE() on some systems
01 Jun 2012, ZS Saad, 3dROIstats, level 1 (MICRO), type 4 (BUG_FIX)
3dROIstats crashed on float dsets with scaling. Not anymore
Problem was scaling brick pointer without mallocizing first.
25 May 2012, ZS Saad, SurfToSurf, level 1 (MICRO), type 4 (BUG_FIX)
Improve auto-name generation and enabled output format specification
23 May 2012, DR Glen, 3dinfo, @auto_tlrc, level 3 (MAJOR), type 4 (BUG_FIX)
Generic space handling corrected for TT_N27 and other spaces
@auto_tlrc would crash with improper generic spaces
Generic space restricted to AFNI view names (orig, acpc, tlrc)
21 May 2012, ZS Saad, SurfToSurf, level 1 (MICRO), type 4 (BUG_FIX)
Microscopic improvement to automatic dset name generation for output dsets
21 May 2012, ZS Saad, ROIgrow, level 1 (MICRO), type 4 (BUG_FIX)
ROIgrow was not taking -spec surface definition
08 May 2012, ZS Saad, 3dSeg, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory leak problem
07 May 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Coordinate transformations in atlas access
Coordinates were not transformed properly if an inverse affine
transformation was required for the case of atlases in another
space than the dataset.
04 May 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 4 (BUG_FIX)
submitting updates from Rayus
Updates are in changelog.
01 May 2012, RW Cox, mri_stats, level 1 (MICRO), type 4 (BUG_FIX)
Fixed student_t2z problem with very tiny p values (roundoff error)
26 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made header_name be same as brik_name for NIFTI dsets
Changes were in EDIT_dset_items(), search for April 26
18 Apr 2012, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Patch BLOCK and dmBLOCK to have their old non-unit-peak behavior
New functions UBLOCK and dmUBLOCK now have the unit-peak behavior.
16 Apr 2012, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Increased allocated space for bigmap variables in display.c
This is to stop a a MCW_malloc post-corruption which happens
under certain compiler/OS combinations. No big deal.
12 Apr 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
backport to python 2.2
For files that should work on 2.2, avoid sum() and enumerate().
Thanks to L Broster for reporting problems on python 2.2.
12 Apr 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
backport to python 2.2
09 Apr 2012, DR Glen, whereami, level 1 (MICRO), type 4 (BUG_FIX)
Typo in AFNI_WAMI_MAX_SEARCH_RAD
Wrong name listed in AFNI GUI environment and README.environment
14 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
test for global timing before local, as it looks like bad local
Thanks to P Pallett for reporting the problem.
09 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
added $hemi to rm.mean dset during scaling; added -overwrite_resp to SA2E
Surface analysis would fail on 2nd hemi, as rm.mean dset would exist.Also,
added new '-overwrite_resp S' to @SUMA_AlignToExperiement command.
08 Mar 2012, RW Cox, OpenMP program, level 1 (MICRO), type 4 (BUG_FIX)
Replace memcpy/memset with AAmemcpy/AAmemset
OpenMP has trouble with these, particularly on Mac Lion. Files affected
include:
3dAutoTcorrelate.c 3dDespike.c 3dREMLfit.c
3ddata.h cs_qmed.c mri_blur3d_variable.c
mri_nwarp.c mrilib.h rcmat.c
thd_incorrelate.c
AAmemcpy and AAmemset are defined in mrilib.h. In particular, this gets
rid of the vastly annoying ___builtin_object_size undefined symbol error
message when linking an OpenMP program with llvm-gcc-4.2 on Lion.
07 Mar 2012, RC Reynolds, GIFTI, level 1 (MICRO), type 4 (BUG_FIX)
fixed sizeof in memset of gim (noted by B Cox)
06 Mar 2012, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Option completion killed filename completion. Not anymore.
05 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Recorder saving was crashing for very long filenames. Not anymore.
The shell however will not like very long names and will complain.
05 Mar 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
EDIT_empty: only propagate writable storage_modes
Added is_writable_storage_mode and DSET_STORAGE_MODE.
Thanks to Eli for reporting the problem.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed suma crash after a plot a certain plot freeze sequence
The sequence was: create plot, freeze it, get another open
then close the frozen one. At this point, suma lost control
of the still unfrozen one, so it is practically frozen.
Pressing Freeze twice on that remaining plot cause suma to crash.
None of that occurs anymore.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed cutting plane motion while volume rendering under linux
On Macs, the scroll wheel gives out button 6 and 7, on linux
it is Buttons 4 and 5.
01 Mar 2012, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Some cleanups and tweaks of XmHTML library.
Refresh was not working well when scrolling so I ended up adding a mini
refresh routine that seems to do the trick. XmHTMLRefresh(Widget w)
It is called each time there is a repositioning. Perhaps that is overkill,
but no need to sweat this for now.
27 Feb 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in read_niml_file() that incorrectly set a read_header_only flag
27 Feb 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Bug in combination of multiple affine transformations
Computation error in combining affine transformations
in whereami. Note all default transformations in whereami
do not combine affine transformations. Instead, space
transformations between TLRC and MNI_ANAT spaces are
computed using a 12-piece or a Brett transformation combined
with an affine in two stages.
24 Feb 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 4 (BUG_FIX)
Added number of volume registration regressors to -ort_adjust
13 Feb 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
-orig_vol now forces datum type to be same as that of input.
This fixed a problem with anatomicals ranging in the million(!) to
come up the equivalent of a binary mask with -orig_vol.
13 Feb 2012, RW Cox, 3dPeriodogram, level 1 (MICRO), type 4 (BUG_FIX)
pfact was not static
But apparently worked OK until Ziad initialized it to zero.
10 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Improved snapshot making. Previous bugs were caused by buffer swap problems
This fixed (I hope for good), problems of recording ('r'), continuous
recording (OS X and Linux), and the oversampling.
07 Feb 2012, ZS Saad, 3dcopy, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with 3dcopy HHH.nii TTT+orig not producing output
Problem was caused by new change to EDIT_empty_copy() which
assigned storage mode to that of input dset instead of STORAGE_BY_BRICK
Fix involved setting storage mode per the prefix or view in
EDIT_dset_items()
06 Feb 2012, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit was failing on the view change when target dset is under a path.
Problem was with default catenation of path to DSET_BRIKNAME and
DSET_HEADNAME. Those now contain the path automatically.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Improved (I hope) sub-brick labels. Added FDR too.
Same improvements to all 3dANOVA programs.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed compatibility with .niml.dset data
This required more improvements (I hope) to THD_init_diskptr_names() and
EDIT_empty_copy() for surface-based datasets.
03 Feb 2012, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
updated @AddEdge command to match change to afni_base:shell_com
Done with D Glen.
31 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
also update check for '### ASCCONV BEGIN' in to3d...
Problem noted by J Lewis.
28 Jan 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
look for TSNR* in case of surf analysis
27 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fix inf loop if some sSliceArray entries not set
Also, now there might be junk between ASCCONV BEGIN and ###, grrrrr...
Problem noted by J Lewis.
25 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
back out overzealous -quit changes for now
23 Jan 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Improved logic for assigning ROIs when parent is not present
ROI parent assignment now takes into account last visited surfacein any of
the open viewer, and hemisphere side when appropriate.
23 Jan 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug in display of FRAME bound textures.
Looks like it had to do with depth testing.
12 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed ricor block 3dcalc loop for varying run lengths
11 Jan 2012, RW Cox, 3dhistog, level 1 (MICRO), type 4 (BUG_FIX)
Fix bugs
(a) fbin storing the counts was not always allocated the right length
(b) changed it from int to int64_t to allow for really large datasets
(c) there is no 3rd item
11 Jan 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
dx and dy were reversed in mri_read_dicom.c
Thanks to P Kaskan and F Ye for bringing this up.
30 Dec 2011, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI datasets used to loose their path information upon loading.
This is problematic for a few reasons. For instance, afni ~/tmp/joe.niml
will display the dataset as ./joe.niml. Some internal functions for
conveniently dealing with atlases fail when the path is messed up in this
way. Also, this problem occurred for NIFTI but NOT AFNI native formats
wich resulted in different behaviour for programs like 3drefit.
For example: 3drefit -space MNI ~/tmp/joe.nii is not comparable to
3drefit -space MNI ~/tmp/joe+tlrc. (Actually, that behaviour was patched
on Dec 27 but explicitly setting the path at output. But the fix needed
to happen for other programs so that is now done at the io level.)
27 Dec 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit failed when refitting a NIFTI dset in another directory.
If you did something like 3drefit -space MNI joe/jim/dset.nii
you ended up with a new dataset ./dset.nii as opposed to modifying
the one under joe/jim/ directory
20 Dec 2011, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
-prefix failed when input dset was mastered.
Better use macro PREP_LOADED_DSET_4_REWRITE whenever modifying
a dataset loaded from disk for the purporse of rewriting it.
13 Dec 2011, ZS Saad, plugout_drive, level 1 (MICRO), type 4 (BUG_FIX)
AFNI_drive_switch_* functions discriminated against short prefixes.
09 Dec 2011, RW Cox, afni (imseq.c), level 1 (MICRO), type 4 (BUG_FIX)
Patch weird bug
When the intensity bar popup menu is up, then the user clicks on an
optmenu, then the next time the user button1 clicks in the image viewer
(say to move the crosshairs), the values of last_bx and last_by are lost
(reset to 0) so the move wrong. Solution -- check if button release is
in the same location (or close) as the button press, and only then allow
a move.
09 Dec 2011, RW Cox, 3dttest, level 1 (MICRO), type 4 (BUG_FIX)
Fix sub-brick selection bug
in THD_multiplex_dataset(), the '$' was not treated right -- just set to
999998. Fix is to use MCW_get_thd_intlist() for proper expansion, which
also will add sub-brick label selection capability.
07 Dec 2011, ZS Saad, @FS_roi_label, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug caused by not cleaning tmp files under /tmp/ with -rankmap
This bug should not have affected anyone. It showed up as I
was making @SUMA_Make_Spec_FS process more than one type of
parcellation volume.
02 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Wrote SOLARIS_strcasestr to replace missing strcasestr on SOLARIS
28 Nov 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Fixed function THD_deplus_prefix to improve prefix cleanup
Previous version cleaned +orig but not +orig.HEAD or +orig. for example.
Current one removes +orig +orig. +orig.HEAD +orig.BRIK +orig.BRIK.gz and
corresponding +acpc and +tlrc brethren.
28 Nov 2011, RC Reynolds, 1dnorm, level 1 (MICRO), type 4 (BUG_FIX)
re-enabled use of '-' for stdin/stdout
Requested by R Birn.
21 Nov 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed -ynames in plot of motion/outliers
18 Nov 2011, RW Cox, 3dUndump, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug introduced with -ROImask
17 Nov 2011, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
if dset+orig is anat/func and dset+tlrc is func/anat, 'BAD dataset', man
Altered logic in thd_initsess.c (done with dglen).
17 Nov 2011, RC Reynolds, @ROI_Corr_Mat, level 1 (MICRO), type 4 (BUG_FIX)
fix complaint about unknown options for non-macs
17 Nov 2011, RC Reynolds, 3drefit, level 1 (MICRO), type 4 (BUG_FIX)
changing 'type' should have an effect even if not a bucket
Done with dglen.
16 Nov 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Condition numbers were checked with SQUARES of singular values!
Fixed by changing function matrix_singvals(). Also make clear in 1dsvd
help that -vnorm option is needed to compare singular values with
3dDeconvolve.
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug introduced by cleaning up header_name and brick_name
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
More changes regarding obliquity warnings.
AFNI:
Popups only appear when user is viewing dsets of different obliquity.
See dset_obliquity_angle_diff()
and THD_report_obliquity()
The warnings only appear ONCE per pair of misfits, per afni process.
See AFNI_check_obliquity() for implementation details.
Oblique notices no longer appear on the command line each time you
read a session or switch dsets. To tell you that you are viewing an
oblique dset and that the coords are not quite what they should be,
I added a '*' next to the 'order:' descriptor in the top left corner.
Command Line programs:
In most programs that should not care about obliquity, I add
early under main():
set_obliquity_report(0); /* silence obliquity */
Also, 3dcalc, 3dTcat, 3dbucket, and function THD_open_tcat()
Only complain when obliquity between dset pair differs.
The check is done right after checking for grid matching with
EQUIV_DATAXES
10 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Turned off obliquity popup warning when Ulay and Olay angles are similar
AFNI issues warning when obliquity differs for a pair of viewed sets.
It does not repeat warnings for a certain pair. It only output one set
of warnings per dataset when 'switch ulay' is set, although I'd love to
get rid of that habit as soon as possible.
10 Nov 2011, ZS Saad, 3dinfo, level 1 (MICRO), type 4 (BUG_FIX)
Many new options for selective information.
07 Nov 2011, DR Glen, lost last character in sub-brick labels, level 2 (MINOR), type 4 (BUG_FIX)
Fixed miscount of characters
03 Nov 2011, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Allow refitting of some attributes
Some attributes like IJK_TO_DICOM_REAL and DELTA were not
being updated correctly with the original values remaining
in the dataset
02 Nov 2011, ZS Saad, 3dfim+, level 1 (MICRO), type 4 (BUG_FIX)
Turned off scaling for Best Index in output dset
26 Oct 2011, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fixed bug where AFNI sent the max voxel to suma despite threshold
In BYTE and SHORT datasets the maximum voxel always got sent to
suma, even if the threshold was higher than the maximum value in
the dataset.
13 Oct 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
-omask failed if atlas was stored in float type.
13 Oct 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Added support for -atrstring operation on NIFTI datasets
This required making changes to THD_init_diskptr_names functions
and a few more of its colleagues.
13 Oct 2011, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fixed error in computing with un-centered covariates
inv[Xt*X] matrix not computed correctly in mri_matrix_psinv_pair()
function.
06 Oct 2011, RC Reynolds, 3dMean, level 1 (MICRO), type 4 (BUG_FIX)
linux_xorg7_64 had optimizer error (and crashed), so altered loop method
Thanks to P Kim for reporting the problem.
05 Oct 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 4 (BUG_FIX)
do not re-create proc script on proc execution
13 Sep 2011, DR Glen, whereami, level 1 (MICRO), type 4 (BUG_FIX)
Added trivial ability to invert identity transformation
06 Sep 2011, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_skullstrip option saved obliqued and skullstripped data
Fixed to save only skullstripped
02 Sep 2011, DR Glen, 3dhistog, level 2 (MINOR), type 4 (BUG_FIX)
Handle binning and output of integer and float data differently
Distinguish between integer and float data. Added float and int
options to enforce specified behavior.
Done with Rick Reynolds.
01 Sep 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
get_default_polort: run time should be TR * (NT-1)
This was changed back to TR*NT, to match 3dDeconvolve (3 Oct, 2011).
30 Aug 2011, RC Reynolds, Dimon, level 1 (MICRO), type 4 (BUG_FIX)
update volume delta to mean dz
From text in DICOM files, initial dz values may not be sufficiently
accurate, leaing to 'volume toasted' errors.
Thanks to B Benson for reporting the problem.
30 Aug 2011, DR Glen, Draw Dataset, level 2 (MINOR), type 4 (BUG_FIX)
Draw Dataset plugin incorrect label for current atlas
Fixed current atlas to be updated properly if atlas is
changed.
17 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed some final anat dset assignments
15 Aug 2011, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
altered SUMA_ParseFname for parsing of relative pathnames
Thanks to Ryan of Princeton for reporting the problem.
03 Aug 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
changed aea.py -save_skullstrip to -save_orig_skullstrip
The -save_skullstrip dataset might have an oblique transformation
applied (which would throw off EPI if it is then sent to standard
space). Apply the new option to grab a simple skull-stripped anat.
Thanks to A Ellenstein for reporting it and Z Saad for help understanding.
01 Aug 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Whereami's symbolic notation failed with float valued atlases
This is now fixed. Code also checks for scale factors.
There was another bug waiting to happen with:
!is_Atlas_Named(atlas, "CA_N27_PM"), which is now:
!is_probabilistic_atlas(atlas)
29 Jul 2011, RC Reynolds, 3dUniformize, level 2 (MINOR), type 4 (BUG_FIX)
fixed checks against lower_limit in option processing (since -1 init)
Thanks to A Waite for reporting the problem and cause in the code.
22 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 4 (BUG_FIX)
after blur, rescale noise to be normally distributed
21 Jul 2011, RC Reynolds, edt_blur.c, level 1 (MICRO), type 4 (BUG_FIX)
fixed nz/sigmay typo, found by Patryk (on message board)
20 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed aea.py -epi_base when: aea.py, -volreg_a2 last, variable run lens
thanks to S Brislin and S White for reporting the problem
13 Jul 2011, RW Cox, 3dTcorrMap, level 2 (MINOR), type 4 (BUG_FIX)
Bug in computation of indx
The mask is turned into an index table of active voxel indx[]. However,
constant voxels were removed from the mask AFTER indx[] was created,
which is stupid. This is fixed now, and Zhark will be chastised.
11 Jul 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed case of partial path match to dsets
Problem found by J Jarcho.
08 Jul 2011, RW Cox, AFNI, level 1 (MICRO), type 4 (BUG_FIX)
Tips HTML window crashes on kampos (Solaris)
Debugging shows XmHTML crashed when rendering different-than-normal
fonts. Solution = strip font-changing HTML tags out of file before
display -- only on systems marked as evil in this way.
20 Jun 2011, ZS Saad, @ROI_Corr_Mat, level 1 (MICRO), type 4 (BUG_FIX)
added support for +tlrc input, more debugging messages, -echo option.
17 Jun 2011, RC Reynolds, SUMA_MiscFunc.c, level 1 (MICRO), type 4 (BUG_FIX)
set 0-length BmP array to matching length 3
16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 4 (BUG_FIX)
No longer complains about not finding seed in cases where it should.
16 Jun 2011, RC Reynolds, 3dAutoTcorrelate, level 1 (MICRO), type 4 (BUG_FIX)
allowed very small datasets
08 Jun 2011, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed print and added min_rest to durations in test of -tr_locked
26 May 2011, RW Cox, thd_cliplevel, level 1 (MICRO), type 4 (BUG_FIX)
Problem with overflow when image has tiny float values
This affects a bunch of programs, including any program that has
automasking. In the computation of the cliplevel of a float dataset,
the dataset is scaled to shorts for histogram-ization, and that scaling
is computed as 10000/maxval -- but if maxval is very tiny (say 1e-35),
then the scale factor is float overflow -- which doesn't work so well
farther on. The solution is to compute the scale factor in double
precision. Or to have less silly users.
25 May 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem with TENT and CSPLIN
For non-integer TR, could miss evaluating the last function in a TENT or
CSPLIN series because of roundoff error pushing the evaluation time
slightly past the 'top' value. This is bad if the function is 1 at
exactly this value, as the last functions are here. Solution was to
change the test to allow evaluation at values slightly larger than
'top'.
25 May 2011, RW Cox, thd_zzprintf, level 1 (MICRO), type 4 (BUG_FIX)
Patched to avoid string overruns for crazy users
24 May 2011, RC Reynolds, 1dplot, level 2 (MINOR), type 4 (BUG_FIX)
fixed plotting of varying length time series
18 May 2011, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Node value now updates when switching dsets while viewing surf patches.
04 May 2011, RC Reynolds, to3d, level 1 (MICRO), type 4 (BUG_FIX)
fixed case of simult tpattern (so time_dep, but ui.tpattern is not set)
Problem noted by J Ostuni.
02 May 2011, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
added nul-termination and a.b[.d]+ rules for checking Siemens slice times
Problem noted by D Kravitz and S Lee.
27 Apr 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 4 (BUG_FIX)
Fixed nx!=ny error in NN2 and NN3 clusterization
22 Apr 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if manual tlrc and -volreg_tlrc_adwarp, also transform extents mask
Noted by J Britton.
Also, if -regress_reml_exec, insert 3dClustSim table in stats_REML.
Noted by R Momenan.
14 Apr 2011, RC Reynolds, thd_atlas.c, level 1 (MICRO), type 4 (BUG_FIX)
for solaris, apply #def strcasestr strstr
11 Apr 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed lost warnings for no sid/gid
29 Mar 2011, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in default view of flat surfaces.
The problem manifested itself when large rotations were present
in the transform of the sv volume, resulting in flat meshes
being incorrectly labeled as spherical.
29 Mar 2011, ZS Saad, ConvexHull, level 2 (MINOR), type 4 (BUG_FIX)
Fixed error with proj_xy option.
24 Mar 2011, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug for case of MNI_ANAT space as not processed
22 Mar 2011, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
nwarp_pass != nwarp_type :-(
Causing bug in application of nonlinear warps from external files.
22 Mar 2011, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
mri_read_dicom: if there is no vrCode, skip explicitVR
19 Mar 2011, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug for case master_dset2_dxyz was accidentally ignored
14 Mar 2011, DR Glen, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bugs when switching between ROI and continuous overlay datasets
Colorscale (scale, range) is restored with continuous overlay dataset.
Need to set AFNI_INT_CMAP or AFNI_INT_PBAR to use.
09 Mar 2011, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed bug writing comment text in 3dD script
Problem noted by Z Saad and P Kaskan.
04 Mar 2011, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug with 1-sample results in -paired run
Forgot to turn off the 'paired' opcode for the 1-sample (no covariates)
analyses, so results were all zero!
03 Mar 2011, RW Cox, mri_nstats.c, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in correl_xxx functions
Didn't allow nort == 0, which is a mistake; the real constraint is
nfit+nort >= 1. Fixed for Yisheng Xu of NIDCD.
02 Mar 2011, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Clusterize: attempt to fix Flash bug
If 2 controllers are open (and crosshairs are locked together), then
Clusterize Flash doesn't work right. This problem is rooted in an
interaction of the way the clusterized dataset is stored and the way the
locks are carried out. This change is an attempt to fix this -- let me
know if it introduces problems -- the code for these things is
complicated and hard to figure out (and I wrote it!).
I know that there is a clusterize display bug with 2 controllers open to
the same overlay -- that is, the clusterized overlay may suddenly become
un-clusterized and then go back to the clusterized state. This is also
related to the above interaction, but I don't see how to avoid this
without a major restructuring of the clusterization mechanics in AFNI,
and I just don't think this issue is worth the effort.
14 Feb 2011, RW Cox, 3dUndump, level 1 (MICRO), type 4 (BUG_FIX)
Fix comma -> blank conversion
Also make semicolons and colons into blanks.
Skip any line starting with an alphabetic character.
27 Jan 2011, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fixed problem in THD_add_bricks when dset in AFNI is not malloc-ed.
24 Jan 2011, RW Cox, afni_setup.c, level 1 (MICRO), type 4 (BUG_FIX)
Re-definition of pre-defined colors
Before this fix, when a user re-defined a pre-defined color in a
***COLORS section, this would go into a new entry for later setup in
MCW_new_DC. But later, the duplicate labels (e.g., 'yellow') would
cause only 1 entry to actually be created -- which would screw up the
indexing of later new colors that were actually created de novo. This
was fixed by re-defining the reused color entries immediately.
20 Jan 2011, RW Cox, 3dClustSim, level 2 (MINOR), type 4 (BUG_FIX)
Small ROI masks could give weird and wrong results
Problem was when a desired alpha level (say 0.10) simply couldn't be
found -- e.g., only 6% of simulations had ANY above-threshold voxels in
the mask. Bad-ositiness ensued since the program didn't check for this
case. Now it checks, uses N=1 as the result in such cases, and
stderr-ifies a warning message also.
The problem with developing software is users. If we didn't have them,
life would be much easier.
18 Jan 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 4 (BUG_FIX)
Fix NN buglets identified by Nick Oosterhof.
07 Jan 2011, RC Reynolds, rickr/Makefile, level 1 (MICRO), type 4 (BUG_FIX)
Dimon: forgot to reconcile use of expat (with LGIFTI)
06 Jan 2011, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fix crash when using '-img' with dataset files (.HEAD or .nii)
Problem was mri_imcount didn't give a correct count, but mri_read_file
did. Easily patched up in time for tiffin. And we take tiffin mighty
durn early in these parts, buckaroo.
06 Jan 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Fix problem with auto-catenation of datasets with length 1
Bug is that each dataset is a separate run, so you have lots of baseline
models! Patch is to find shortest length of the component datasets --
if this is 1, then treat them as one big happy run. Also, the new
-noblock option will do the same regardless of the structure of the
inputs.
06 Jan 2011, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
ComputeObliquity() mosaic shift should be dcK*(nK-1)/2 in each direction
04 Jan 2011, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
Fixed SurfSmooth to work with the combination HEAT07+Sparse Dsets+cmask
The problem was caused by a bad masking operation at the detrending
function when sparse datasets with cmask option are used. The detrending
is used to estimate the FWHM in the blurmaster. As a result, SurfSmooth
would not converge under such circumstances.
In addition there was an optimizer related bug in the macro SUMA_COL_FILL
Thanks to Christopher Ackerman from JHMI for reporting the bug.
04 Jan 2011, ZS Saad, SurfFWHM, level 2 (MINOR), type 4 (BUG_FIX)
Fixed SurfFWHM which had the same masking problem as SurfSmooth.
03 Jan 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
Modified decode_*linebuf to better treat the 'i' character in 1D files
14 Dec 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problem with timing file tests on 'empty' files with '*'
problem noted by C Deveney and R Momenan
24 Nov 2010, ZS Saad, 3dTcat, level 1 (MICRO), type 4 (BUG_FIX)
3dTcat was forcing sub-brick selection at times
Say each of dset1 and dset2 has 10 subbricks.
A command like this:
3dTcat dset1+orig[0..8] dset2+orig
used to produce a dataset that is 18 sub-bricks, not
19. That is because the [0..8] selection was applied
to dset1 and all subsequent dsets on the command that
did not explicitly have selectors in their name.
18 Nov 2010, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 4 (BUG_FIX)
fix for '*' in max 1 stim per run case
18 Nov 2010, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed stim_files to stim_times conversion after multi_basis change
problem noted by M Weber
17 Nov 2010, RW Cox, many programs, level 1 (MICRO), type 4 (BUG_FIX)
Move AFNI_OMP_START / _END macros outside of OpenMP sections
Otherwise tracing control on/off doesn't work - D'oh!
04 Nov 2010, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed print problem in -show_indices
Problem noted by Mingbo Cai.
01 Nov 2010, ZS Saad, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
3dBrickStat's percentile option did not work with byte datasets
28 Oct 2010, RC Reynolds, 3dMean, level 1 (MICRO), type 4 (BUG_FIX)
do not proceed in case of no input datasets
27 Oct 2010, RW Cox, cs_symeig, level 1 (MICRO), type 4 (BUG_FIX)
Patch failure on Mac gcc in svd_double
Mac OS X gcc compilation of svd function can produce bad results -- NaN
values -- when there are too many all zero columns. Solution: check for
NaNs in the result, then switch to 'slow' mode AND fill all zero columns
with tiny random values.
22 Oct 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed rendering of spheres, which were affected by ambient light.
Thanks to MSB for the complaint.
20 Oct 2010, RC Reynolds, thd_niftiwrite.c, level 1 (MICRO), type 4 (BUG_FIX)
brick stats to intent codes was off by 1 index
Problem noted by P Kohn.
16 Oct 2010, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed timing_to_1D fractions
01 Oct 2010, DR Glen, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Overlay color autorange, range settings not initialized properly
24 Sep 2010, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug in afni_receive.c
When a receiver shuts down its own reception, then the pointer to the
receive structure is freed. In AFNI_process_alteration(), this caused
the time STAMPER macro to de-ref the NULL pointer. STAMPER was modified
to avoid this problem, which would cause afni to crash if the user
switched to +tlrc during drawing in +orig. This, of course, is Daniel
Glen's fault (because surely I am guiltless).
22 Sep 2010, RW Cox, 3dttest++, level 1 (MICRO), type 4 (BUG_FIX)
Ensure no division by zero if covariates matrix has all zero column
21 Sep 2010, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fix memory leak and paired t-test bug.
17 Sep 2010, RC Reynolds, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
init workspace with 0
Trouble noted by M Choi
13 Sep 2010, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 4 (BUG_FIX)
Add missing free(xar) to 1-sample t-test loop [oops]
10 Sep 2010, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 4 (BUG_FIX)
removed extra endif's in case of $label_dir
07 Sep 2010, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash caused by bad function prototype.
Crash only occurred on linux. Thanks to P. J. Kohler for
tests and bug report.
03 Sep 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed inappropriate read in SUMA_Draw_SO_Dset_Contours
This bug had caused a crash on one machine, but had the potential
for bad surprises in the future.
30 Aug 2010, RC Reynolds, @CheckForAfniDset, level 1 (MICRO), type 4 (BUG_FIX)
replaced use of {$var} with ${var}
Problem noted by R Mruczek.
30 Aug 2010, RC Reynolds, 3dVol2Surf, level 1 (MICRO), type 4 (BUG_FIX)
check for -sv dataset before proceeding
26 Aug 2010, ZS Saad, @auto_tlrc, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug in @auto_tlrc in usage 2 mode AND with no suffix
There was a bug in @auto_tlrc for the last 2 months:
from June 30, 2010 until August 26, 2010.
It occurs only when using auto_tlrc in:
usage 2 mode
AND
with -suffix omitted, or set to NONE.
This bug does not affect your data if you had used adwarp -apar,
or if you put your data in TLRC space via afni_proc.py,
or align_epi_anat.py.
The bug essentially results in a renaming of your follower dataset,
without the spatial transformation. So, if you were applying the
transform to epi+orig, it practically got renamed to epi+tlrc.
Despite the +tlrc in the name, epi+tlrc would still be in +orig
view and you no longer have epi+orig on disk.
Examples of affected commands would be:
@auto_tlrc -apar anat+tlrc -input epi+orig
or
@auto_tlrc -apar anat+tlrc -suffix NONE -input epi+orig
The script did produce Error messages but it failed to stop.
If you think you ran the buggy command (a clear symptom would be
missing +orig datasets AND bad alignment in TLRC of course), you
must download the latest binaries and rerun @auto_tlrc after you
have recreated the +orig files. You can also just get @auto_tlrc
at the link below.
Sorry for this, I had tested complicated option combinations on
the last release, but all tests had used the -suffix option.
()
Binaries postdating this message will contain the new script.
You can also get a corrected version of @auto_tlrc at this link:
Thanks To James Blair for finding the bug.
09 Aug 2010, ZS Saad, MapIcosahedron, level 1 (MICRO), type 4 (BUG_FIX)
Changed 2 sprintf lines writing and reading from same address.
06 Aug 2010, ZS Saad, 3dSetupGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug with LRpairs when time series had different lengths.
Also fixed minor bug with error message about data size
06 Aug 2010, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Tiny changes to functions prettyfying numeric outputParticularly functions approximate_number_string, and
commaized_integer_string, and macro MEMORY_CHECK in 3dREMLfit
05 Aug 2010, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed crash when using group instant correlation on 1 surface.
04 Aug 2010, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Restore 'jump to' capability when selecting a marker
Removed accidentally when disabling the popup marker toggles.
03 Aug 2010, RC Reynolds, afni_history, level 1 (MICRO), type 4 (BUG_FIX)
fixed -check_date test to see if version is current
This problem affects afni_proc.py script execution.
02 Aug 2010, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed default naming for interactive dsets.
The older naming, based on label, rather than filename
created some conflicts under certain cases.
Repair job in SUMA_dot_product.
28 Jul 2010, RC Reynolds, zfun.c, level 1 (MICRO), type 4 (BUG_FIX)
fixed small typos in the case of HAVE_ZLIB not being defined
- zzb64_to_array (return) and array_to_zzb64 (missing arg)
27 Jul 2010, RC Reynolds, thd_table.c, level 1 (MICRO), type 4 (BUG_FIX)
strtod typo
26 Jul 2010, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
Mean calculations were off for large clusters with large values.
19 Jul 2010, RC Reynolds, 3dFWHMx, level 1 (MICRO), type 4 (BUG_FIX)
fixed -arith mean
16 Jul 2010, RC Reynolds, afni, level 1 (MICRO), type 4 (BUG_FIX)
added legendre to forced_loads array for plugin use
09 Jul 2010, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Skip FDR masking if dataset isn't really 3D
08 Jul 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed striping with contour objects
07 Jul 2010, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixes for large files (noted/investigated by M Hanke and Y Halchenko)
- fixed znzread/write, noting example by M Adler
- changed nifti_swap_* routines/calls to take size_t
07 Jul 2010, RC Reynolds, nifti_tool, level 1 (MICRO), type 4 (BUG_FIX)
fixed nt_read_bricks bsize computation for large files
07 Jul 2010, RC Reynolds, NIFTI, level 1 (MICRO), type 4 (BUG_FIX)
fixed znzread/write to again return nmembers
Also, added M Hanke's update to CMakeLists.txt for new release number.
10 Jun 2010, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed copying EPI and anat as NIFTI
08 Jun 2010, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed partitioning without zeros
27 May 2010, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fix bug in paired t-test for covariates regression
27 May 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed use of -volreg_regress_per_run and -regress_censor_motion pair
Problem found by D Drake.
19 May 2010, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Bug: 'filename' copy from argv[] can be too long for 1D: input
Especially if the user is named Handwerker. Solution: compute length of
'filname' before malloc-izing, vs. fixed length THD_MAX_NAME.
19 May 2010, RC Reynolds, Makefile.*, level 2 (MINOR), type 4 (BUG_FIX)
add CCOLD to all for compiling nifticdf.o on linux_xorg7_64 using gcc v3
This is a bug in the gcc compiler code, not in AFNI. So the workaround
is to compile nifticdf.o with a different version of the compiler.
The gcc compiler versions 4.1-4.3 (at least) had an optimization bug
when compiling nifticdf.o. The result was an inaccurate conversion
from F-stats to p-values (in some cases).
Test with the command: cdf -t2p fift 1.0 10 100
good result: 0.448817, bad result: 0.0472392
Problem found by L Thomas and B Bones.
17 May 2010, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Program would crash when only -Obuck given, no -Rstuff
Problem was that GLT data structure setup was done in the Rstuff loop,
and if no Rstuff datasets are computed, then doing GLT stuff in the
Ostuff loop would crash. Fix: test if GLTs are added to the REML setup
structures in the Ostuff loop, and add them if they aren't already
there.
14 May 2010, RW Cox, 3dMean, level 1 (MICRO), type 4 (BUG_FIX)
Fix scaling problem
As in 3dcalc: if scaling is not forced (no -fscale or -gscale) but is
optional (no -nscale, either), then check if the values in a sub-brick
are non-integral -- if so, do scaling anyway to minimize truncation
problems.
10 May 2010, RC Reynolds, ktaub.c, level 1 (MICRO), type 4 (BUG_FIX)
allow for build on SOLARIS_OLD
06 May 2010, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fix NULL pointer de-reference from renderer
When colorscale is changed to one of the ROI colormaps, Ziad the Wise
added a 'feature' to automatically change the im3d viewer data range for
the user's convenience. However, this doesn't work when the colorscale
isn't in an im3d -- such as in the renderer.
02 May 2010, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
Fixed Instacorr update failure when A_ICOR dset is present on disk.
21 Apr 2010, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
-nodtrnd option was setting polort to 1, as opposed to 0.
12 Apr 2010, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Added AFNI_GUI_WRITE_AS_DECONFLICT to modify interactive 'Write' overwrite.
The default is to have the interactive 'Write' buttons overwrite existing
volumes. If this env variable is set to YES, the 'Write' behaviour follows
env AFNI_DECONFLICT
12 Apr 2010, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Made InstaCorr SeedJump work with GroupInCorr
08 Apr 2010, RW Cox, 3dBandpass, level 2 (MINOR), type 4 (BUG_FIX)
Fix -localPV implementation
29 Mar 2010, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
Make sure auto_tstring is set to something reasonable
23 Mar 2010, ZS Saad, 1dplot, level 1 (MICRO), type 4 (BUG_FIX)
Fixed unreported bug related to wintitle variable.
18 Mar 2010, ZS Saad, RetroTS, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash in function remove_PNduplicates
17 Mar 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed timing_to_1D when some runs are empty
Problem found by L Thomas and B Bones.
16 Mar 2010, RC Reynolds, 3dbucket, level 2 (MINOR), type 4 (BUG_FIX)
fixed getting incorrect FDR curves (noted by D Glen)
09 Mar 2010, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
-isomerge and -isovalue options were being ignored
08 Mar 2010, ZS Saad, 3dTcat, level 2 (MINOR), type 4 (BUG_FIX)
Program was not working with string label sub-brick selection
04 Mar 2010, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash with paired t-test opcode
Didn't switch to 1-sample mode when opcode was for paired, but no second
data vector was passed in. This, of course, is Mike Beauchamp's fault.
09 Feb 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed silly bug introduced in previous version
isdigit() method not called properly (Thanks Rick)
14 Jan 2010, RC Reynolds, 3dVol2Surf, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash w/labels on '-map_func seg_vals' -> NIML
Problem found by Swaroop at Dartmouth.
12 Jan 2010, RC Reynolds, 2dImReg, level 1 (MICRO), type 4 (BUG_FIX)
Fixed crash if ny > nx. Go back to failure and ponder fix.
07 Jan 2010, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
stdint.h should not be included on a SOLARIS_OLD system
06 Jan 2010, RC Reynolds, thd_intlist.c, level 2 (MINOR), type 4 (BUG_FIX)
fixed sub-brick selection of datasets without labels (e.g. NIfTI)
15 Dec 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 4 (BUG_FIX)
Fixed 2 problems with -ort option
1) It didn't work, since the wrong array name was used :-(
2) It could fail, since the detrend routine didn't like collinear orts
-- replaced it with one that is happier with such things.
14 Dec 2009, DR Glen, McRetroTS, level 2 (MINOR), type 4 (BUG_FIX)
Variable Opt parameters were not parsed correctly
Options structure fields should be added correctly into Opt structure
12 Dec 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
modify parsimonious fit index to be based on null model
Previous calculation used chi-square from minimum model without adjusting
for number of parameters in model.
01 Dec 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Ignore triangles from Caret with nodes that have all zero coords
Not doing so results in bad display of some flat meshes because
the .topo file contains triangles with nodes that appear masked by
0.0 0.0 0.0 in the .coord file
01 Dec 2009, ZS Saad, @SUMA_Make_Spec_Caret, level 2 (MINOR), type 4 (BUG_FIX)
Improved script to make it pick up new naming convention.
30 Nov 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
afni crashes on short ANALYZE file from double fclose()
24 Nov 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 4 (BUG_FIX)
Stopped writing empty attributes which caused trouble in AFNI.
Empty attributes make AFNI halt the parsing of the header.
24 Nov 2009, RW Cox, thd_atr.c, level 1 (MICRO), type 4 (BUG_FIX)
Allow 'count = 0' in attributes
Formerly was a fatal error. Now just skips to next attribute. For
Ziad.
23 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Workaround for connection drop between AFNI and SUMA in Shared Memory Mode.
Env SUMA_AttemptTalkRecover allows SUMA to recover from drop.
This ENV is set by default to No.
23 Nov 2009, ZS Saad, afni, level 1 (MICRO), type 4 (BUG_FIX)
A couple of small fixes to drive_switch functions.
The problem with with sscanf reading past string end
in certain cases.
19 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed recorder lag on OS X machines.
On OS X platforms, the 'r' or 'R' recording modes
used to record the previous image it seems.
06 Oct 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
More bug fixes related to ROI loading, and OSX's GLX problem
24 Sep 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed crashes on OS X 10.5 caused by OS X's buggy GLX implementation
16 Sep 2009, RC Reynolds, 3ddot, level 2 (MINOR), type 4 (BUG_FIX)
de-meaning data causes permission-based seg fault, apply means upon read
Problem found by Giuseppe Pagnoni.
08 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Properly allows post-transformation matrix
03 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes for certain combinations
Allowed BASE and SOURCE specification for oblique data
Allowed 3dWarpDrive volume registration with mean/max base
Removed anatomical output with oblique data and only epi2anat
28 Aug 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed make_CENSORTR_string, comma delimitation needs run: prefix
27 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed motion_ prefix in '3dDeconvolve -censor'
Problem found by B Bones.
24 Aug 2009, RW Cox, mrilib.h, level 1 (MICRO), type 4 (BUG_FIX)
CABS macro fails if complex number has huge components
This is Larry Frank's fault, of course.
06 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problems found by I Mukai and K Bahadur
- fixed -volreg_align_to base as applied in align_epi_anat.py
- fixed blur 'averages' computation when only one run
29 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed creation of extents mask when only 1 run
27 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use -slibase_sm instead of -slibase in 3dREMLfit
23 Jul 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug when all vectors are zero.
30 Jun 2009, RW Cox, various 3D programs, level 1 (MICRO), type 4 (BUG_FIX)
Remove keywords propagation stuff
e.g., 3dTcat and 3dbucket
Also, fix keywords printout buffer overflow in thd_info.c
29 Jun 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
Fix memcpy bug in data extraction when using OpenMP. Ugghh.
25 Jun 2009, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed dz sent to RT plugin for oblique datasets
25 Jun 2009, RC Reynolds, 3dretroicor, level 1 (MICRO), type 4 (BUG_FIX)
pass MRI_IMAGE structs without const
24 Jun 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applied print changes from B Feige (26 files):
3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c
suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c
SUMA/ SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c
SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c
SUMA_ParseCommands.h SUMA_SphericalMapping.c
SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c
SUMA_compare_surfaces.c SUMA_xColBar.c
svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c
23 Jun 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
added 4 checks of alloc() returns
17 Jun 2009, DR Glen, RetroTS.m, level 2 (MINOR), type 4 (BUG_FIX)
Number of TRs found incorrectly because of rounding
15 Jun 2009, RW Cox, AlphaSim, level 1 (MICRO), type 4 (BUG_FIX)
OpenMP: cdfnor() and other functions are not thread-safe
Make use of cdfnor() 'critical'. Longer term: should patch the nifti
CDF functions to avoid static variables where possible.
15 Jun 2009, DR Glen, BrikLoad.m, level 2 (MINOR), type 4 (BUG_FIX)
Typo in BrikLoad
Gremlin got to Pixy
11 Jun 2009, RW Cox, zgaussian, level 1 (MICRO), type 4 (BUG_FIX)
'long' should be 'int' on 64 bit systems, when doing bit twiddling
28 May 2009, RC Reynolds, strblast, level 2 (MINOR), type 4 (BUG_FIX)
partial words had resulted in skipping ahead
found by R Notestine of UCSD
22 May 2009, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Check if im3d->fim_now is NULL in AFNI_func_overlay()
21 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Additional check for caret-version string
It seems that the syntax for caret-version has changed
slightly and was being missed by SUMA. As a result, Caret
surfaces were not being properly aligned with the volumes.
14 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
no 'rm rm.*' if such files were not created
14 May 2009, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed -glt_label > -num_glt error message and -dmbase def for polort >= 0
12 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed 'cat' of 'across-runs' ricor regressors
08 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Better display of ROI contours on patches
Suma now correctly handles ROI display when the ROIs
contain nodes that are not in the patch. Also, on flat surfaces,
ROI contours are drawn raised so that they float over flat surfaces.
08 May 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
small cut-n-paste errors in db_mod.py and afni_util.py
05 May 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 4 (BUG_FIX)
Added 'd' and 'j' keys
01 May 2009, RW Cox, thd_bandpass.c, level 1 (MICRO), type 4 (BUG_FIX)
modified to make it actually work, including lowpass and highpass
01 May 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
Tree growth fix
Fixed bug in tree growth and improved output text
29 Apr 2009, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
-detprefix_* options now do something!
29 Apr 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash when using -it option for geometry smoothing
29 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
when opening -geomparent, allow for known non-afni extensions
22 Apr 2009, DR Glen, @AddEdge, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique edge display
Fixed bug with oblique data in edge display
16 Apr 2009, RW Cox, All, level 2 (MINOR), type 4 (BUG_FIX)
Inadvertent recursion in afni_environ.c now blocked.
14 Apr 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
niml ROI files with empty ROI no longer crash suma/ROI2dataset
14 Apr 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 4 (BUG_FIX)
possible to have truncation cause a negative variance in stdev_ub
13 Apr 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
fixed bug in printing censor message for -addbase and -slibase
11 Apr 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fixed use of -regress_errts_prefix with blur est
10 Apr 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Error in processing -slibase file with censoring
Typo in replacing input image with censored image caused the end of the
world (SEGV crash).
02 Apr 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 4 (BUG_FIX)
Fixed a little bug in 3dLocalSVD.
26 Mar 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
small array fix for older python in write()
16 Mar 2009, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
malloc extra val in case of percentile truncation
06 Mar 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
if mri_automask_image() input is not really 3D, only apply clip
3dD uses automask for misfit warning, let this apply to niml.dset
05 Mar 2009, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
free vox_warp via KILL_list rather than directly when deleting dataset
Fixes afni crash: set acpc markers -> acpc view -> orig view
-> new markers -> acpc view -> death ...
04 Mar 2009, RW Cox, 3ddata.h, level 1 (MICRO), type 4 (BUG_FIX)
Fix usage of realpath() array dimension with RPMAX macro
20 Feb 2009, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
many inits to appease lesstif and Xt (w/Ziad)
13 Feb 2009, RC Reynolds, dmat44.c, level 1 (MICRO), type 4 (BUG_FIX)
cut-and-paste error ...
11 Feb 2009, RW Cox, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
replace DMAT_svdrot_old with DMAT_svdrot_newer
Old function fails sometimes, making the output rotation be garbage and
producing junk image results; the newer one seems more robust.
10 Feb 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
fixed premature mask free-ing bug
05 Feb 2009, RW Cox, 3dREMLfit, level 1 (MICRO), type 4 (BUG_FIX)
typo ==> DOF params for Full_Fstat weren't in output dataset
04 Feb 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fixed norm reversal application and norm dir check computation
Thanks to Xiaopeng Zong for finding these problems.
03 Feb 2009, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
No longer crashes with old format ROIs
03 Feb 2009, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Fixed free-related error messages on OS X
These errors were generated because some pointers
were allocated with MCW_MALLOC and freed without it.
solution was to include mcw_malloc.h in coxplot and
gifti_choice.c
13 Jan 2009, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI should now be Lesstif compliant
Made numerous changes with Rick Reynolds. The biggest modification
regards buttons inside popup menus. Those buttons are no longer
inside rowcolumn widgets and had to be directly managed by afni.
02 Jan 2009, RC Reynolds, afni_environ.c, level 1 (MICRO), type 4 (BUG_FIX)
fixed bad lvalue when USE_TRACING is not defined
also fixed define for USE_TRACING in solaris and cygwin Makefiles
31 Dec 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
fix for lesstif crash on 'where am i', along with ziad
23 Dec 2008, RW Cox, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
Program wouldn't read a -stim_times file that was all '*'
Actual change was in mri_read.c.
19 Dec 2008, DR Glen, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Slice timing for children can be ignored
If child epi data does not need slice timing correction, script will
continue instead of exiting
11 Dec 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed -slibase bug.
Oopsie. -slibase didn't work properly with more than 1 added column per
slice. Also, per the request of ZSS, you can now input more than 1
column set per image file, in repetitive slice order:
0 1 2 3 0 1 2 3 0 1 2 3
if there are 4 slices in the dataset, for example.
09 Dec 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed (potential) SUMA crash when Draw ROI interface is first opened
08 Dec 2008, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
SUMA works now with LESSTIF, interface is almost the same as in MOTIF
02 Dec 2008, ZS Saad, general, level 1 (MICRO), type 4 (BUG_FIX)
Environment vars. set in the shell override those in .afnirc or .sumarc
07 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
tlrc view handling
fixed view name of tlrc output with tlrc_master set to SOURCE
06 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique children handling
fixed combination of oblique with child epis for epi2anat output
04 Nov 2008, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 4 (BUG_FIX)
skip all zero sub-bricks in the blurmaster - for Tomski Rosski
30 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
AddEdge with epi2anat
fixed AddEdge option for epi2anat output
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
actually applied -min_rest, sorry...
23 Oct 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 4 (BUG_FIX)
removed reference to cdflib, for 'make afni_src.tgz'
15 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed errts (etc) outputs: censored values not set to zero!
14 Oct 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
If source=scaled shorts, then output will be scaled as well.
18 Sep 2008, RW Cox, Vecwarp, level 1 (MICRO), type 4 (BUG_FIX)
Only require +orig dataset if user actually NEEDS it
Program required the +orig version of the -apar dataset, which is needed
for SureFit work, even if it wasn't actually going to be used. Not any
more.
16 Sep 2008, RC Reynolds, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
allow attribute editing of NIfTI datasets
10 Sep 2008, RC Reynolds, plug_realtime, level 1 (MICRO), type 4 (BUG_FIX)
re-added sending of magic_bye string on MP socket close
02 Sep 2008, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
Starting sphere center was incorrectly initialized
29 Aug 2008, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
Uninitialized pointer in 3ddelay
28 Aug 2008, RW Cox, miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Fixed 'is used uninitialized' errors in several codes.
Via the new macro ZZME() in 3ddata.h, which zeros out a struct.
27 Aug 2008, DR Glen, 3danisosmooth, level 2 (MINOR), type 4 (BUG_FIX)
Initialized variable for 3D case
26 Aug 2008, RC Reynolds, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
initialized ntask in all cases
15 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
init graph->grid_spacing, to prevent potential div by 0 via DRIVE
14 Aug 2008, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
do not automatically print -max along with -var
05 Aug 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
re-added the un16 fix from July 1
28 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 4 (BUG_FIX)
alter check for bad socket: use tcp_alivecheck over tcp_writecheck
15 Jul 2008, RW Cox, count, level 1 (MICRO), type 4 (BUG_FIX)
Make '-suffix' work correctly for last item (per Fred Tam).
Also, make '-sep' and '-suffix' work as separate items,
instead of as synonyms for the same thing, which is stoopid.
15 Jul 2008, DR Glen, 3dWarp, level 2 (MINOR), type 4 (BUG_FIX)
Print correct obliquity transformation matrix
03 Jul 2008, RC Reynolds, plug_drawdset, level 1 (MICRO), type 4 (BUG_FIX)
edt_dset_items.c: for .hdr, use .img brick file, storage_mode = BY_NIFTI
01 Jul 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fixed crash in case of mosaic and un16, no longer having im data
Problem found by R. McColl.
18 Jun 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes - duplicate master options, mislabeled variable
06 Jun 2008, RC Reynolds, plug_crender, level 2 (MINOR), type 4 (BUG_FIX)
integral threshold was off by 1
29 May 2008, RC Reynolds, model_demri_3, level 1 (MICRO), type 4 (BUG_FIX)
help update to clarify use of AFNI_MODEL_D3_R1I_DSET
22 May 2008, RC Reynolds, 3dTshift, level 2 (MINOR), type 4 (BUG_FIX)
with -rlt, slices without any time shift must still be processed
problem noticed by Jie Huang
21 May 2008, RW Cox, afni, level 1 (MICRO), type 4 (BUG_FIX)
Put -1dindex into '3dclust' output from Clusterize report. Oops.
21 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed incorrect scaling in Cp computation
The error was introduced on April 8, 2008.
15 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory corruption when using more than 20 regressors
14 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed application of decay term
14 May 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
1D file names for child epi data,micro changes
08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed memory corruption caused by improper declaration of combName
07 May 2008, RC Reynolds, plug_3Ddump_V2, level 2 (MINOR), type 4 (BUG_FIX)
allow 4D datasets to be opened (so that buckets are again usable)
PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES...
01 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
treat RESID_CT as Ct(t), not C(t)
30 Apr 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 4 (BUG_FIX)
replaced make_stim_files with make_stim_times.py in help
24 Apr 2008, ZS Saad, SurfSmooth, level 1 (MICRO), type 4 (BUG_FIX)
Fixed leaky SurfSmooth.
Leak was from one of fin_float pointers in Head07
Also found leak in THD_extract_detrended_array and a few
more small leaks in other SUMA function. Valgrind is good.
16 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
multiple changes
Naming conventions for tlrc output, generic shell compatible,
regridding options for epi and tlrc epi output
14 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
minor change
3dAllineate options are also applied to epi to anat alignment,
so output EPI datasets get original resolution and type.
08 Apr 2008, RW Cox, 3dTfitter, level 1 (MICRO), type 4 (BUG_FIX)
Deal with ref (LHS) vectors that are very tiny.
Modify thd_fitter.c so that ref vectors that are very tiny compared to
the largest one will not be included in the regression. Per the
unreasonable request of Rasmus Birn.
08 Apr 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 4 (BUG_FIX)
Weighting in LPC cost function
Realized that weighting in computing the LPC was only done on the blok
level computation of the PC. All the blok PC values were averaged
together without weighting. Modified code to use sum of weights over a
blok as a weight for its PC. This can be turned off by setting
environment variable AFNI_LPC_UNWTBLOK to YES (to restore the LPC
function to its previous behavior).
08 Apr 2008, RC Reynolds, 2dImReg, level 2 (MINOR), type 4 (BUG_FIX)
allow zero slices, passing input as result
Choleski factorization would fail on an empty slice. In this case,
return the input slices as the result (instead of crashing).
Done with D Glen.
28 Mar 2008, DR Glen, 3dDTeig, level 2 (MINOR), type 4 (BUG_FIX)
small negative eigenvalues are set to zero as in 3dDWItoDT
This fix avoids FA being set to 0 for those affected voxels
26 Mar 2008, ZS Saad, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
3dvolreg's -1Dmatrix_save was not always accounting for centers of rotation
Now the output of -1Dmatrix_save always matches what one would get for
the first sub-brick from
cat_matvec FRED+orig::VOLREG_MATVEC_000000 -I
26 Mar 2008, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
26 Mar 2008, DR Glen, matrix.c, level 1 (MICRO), type 4 (BUG_FIX)
freed matrix used in matrix_sqrt functions
25 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
ROIs drawn on different surfaces now handled properly
25 Mar 2008, RW Cox, 3dDetrend, level 2 (MINOR), type 4 (BUG_FIX)
-normalize didn't work -- what the hellll was I thinking?
Also, added some help to explain how to use 3dDetrend on 1D files.
25 Mar 2008, RW Cox, 1dnorm, level 2 (MINOR), type 4 (BUG_FIX)
Forgot the sqrt()! kudos to David Perlman.
24 Mar 2008, RC Reynolds, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
applied proper follower dataset orientation and floating point shifts
The shift applied to the child datasets was based on the parent's
orientation. The shifts were also being truncated to integers.
Changed with D Glen.
12 Mar 2008, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX)
Changed crash in SurfaceMetrics when -spec and -i options are mixed.
10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
averages did not include nodes lost to -cmask
Noticed by M Beauchamp.
07 Mar 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 4 (BUG_FIX)
properly ignore empty lines, and exit on short files
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed passing of INDEX_LIST
04 Mar 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
couple of small changes to help the hapless users
* add more informative error message if allocate_memory() fails
* force '-float' if any output prefix is NIfTI-1 format (.nii)
27 Feb 2008, ZS Saad, suma-general, level 1 (MICRO), type 4 (BUG_FIX)
Another bout of initialization and leak fixes based on valgrind's output
The hope is that some weird X behavior is caused by uninitialized
variables.
27 Feb 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed -regress_use_stim_files typo (was -regress_use_stim_times)
25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
fixed application of cluster for sending data to suma
Previously, clustering was only applied when the Olay and Thr sub-bricks
were the same.
29 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Fixed bug in 3dFDR -new handling of mask -- ooooppssssie.
* And bug in FDR curves generated from signed statistics (like t).
28 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Added PRINT_COMPILE_DATE macro to mrilib.h and to a lot of programs'
-help output.
* Fixed 'rule of 15' bug in afni_cluster.c, where the initial display only
showed a max of 15 widget rows, even if there were more clusters, but
the number of rows would be reset correctly on any re-clusterizing.
Problem: didn't initialize maxclu_default at the right location.
* Fixed problem with display of clusterized dataset which is both the
Underlay and Overlay: the Underlay was being shown as the edited
volume, but that looks real bad. Solution: disable vedit feature
in AFNI_dataset_slice() when calling from the 'get anat image' place
in afni.c, and then re-enable it right afterwards.
16 Jan 2008, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Fix clusterize so that too small a value of vmul means just set the
min cluster volume to 2 voxels.
* Unfixed bug: display of clusterized func+tlrc.BRIK when func+tlrc datase
t
is warped from func+orig -- must fix afni_warp.c in this case.
05 Nov 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Insert some sleeping to try to avoid X11 errors that have been reported
(but not seen by me) about XGeometry.
* If DONT_USE_XTDESTROY is #define-d, then XtDestroyWidget() is replaced b
y
XtUnrealizeWidget() -- this is used in the Makefile for linux_xorg7,
where the old bug in that Xt library function seems to have risen
from the dead.
16 Oct 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Small bug in decode_linebuf() in mri_read.c -- if a non-number character
is encountered in non-slowmo mode, infinite loop ensues and that's bad.
Now, such an encounter leads to an immediate break out of the loop.
* Small changes to approximate_number_string() and it's usage in 3dDeconvo
lve.
* Fix to afni_graph.c so that 'Boxes' plot mode turns off 'Double Plot'.
11 Sep 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Modified 3dBlurToFWHM.c to remove scale factors from 'outset' if 'inset'
had them. Oopsie.
16 Aug 2007, RW Cox, Miscellaneous, level 1 (MICRO), type 4 (BUG_FIX)
Older History stuff
* Modify 3dDeconvolve.c to check -stim_times files for 0-1 inputs and for
duplicate times.
23 Sep 2005, G Chen, 3dANOVA2 and 3dANOVA3, level 4 (SUPER), type 4 (BUG_FIX)
Significant modifications in 3dANOVA2 and 3dANOVA3
The changes were made to avoid statistics inflation for general linear
contrasts when coefficients don't add up to 0. See more details at
https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
auto-generated by afni_history on Oct 31 2024