AFNI HISTORY

level 1 and higher

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 -min_level 1 -past_years 2 

---- log of AFNI updates (most recent first) ---- 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()' 31 Aug 2021, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add option -gert_chan_digits, to specify num digits for channel in name 31 Aug 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Change default cost function to 'lpa', from 'ls'. Should be better? There is an opt to change, as necessary.
30 Aug 2021, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) New opts: '-all_roi_zeros' and '-automask_off'. Basically, N ROIs can have NxN mat, even if ROI ave is all zeros.
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.
20 Aug 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -write_tsv_cols_of_interest
19 Aug 2021, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Change top-of-image drawn label to resize font if drawn too large
17 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 6 (ENHANCE) Modified to use OpenMP 3dTfitter.c, thd_fitter.c, and thd_lasso.c
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.
10 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 1 (NEW_PROG) Add -LCB option for block-wise LASSO penalties LCB = LASSO Centro Block The penalty in a block is sum{ ABS[ beta[i] - centromean(beta[i],...) ] } which is intendend to make all the beta[i] in a block shrink towards a common value, rather than towards 0. The intent is to use this with IM regression models from 3dDeconvolve, to reduce outliers in the stimulus-wise beta estimates. 10 Aug 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 5 (MODIFY) No longer worry about even/odd slice output (and remove '-no_fs_prep'). Dealt with an old non-issue.
29 Jul 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 2 (NEW_OPT) Add in @chauffeur_afni functionality: -edgy_ulay.
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 .
26 Jul 2021, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add options -dcx, -dcy, -dcz, dc3 This provides the center of the volumetric grid, in DICOM coords.
22 Jul 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -multi_durations_from_offsets Added on the authority of W-L Tseng.
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.
15 Jul 2021, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Change image overlay label plotting to allow for multiline strings Per DRG: multiline strings, being centered along the y-axis about their point of origin, would be pushed off the top of the image. Fixed by setting the y-coord of the origin point to include a factor for the number of lines. 15 Jul 2021, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT) add -empty_is_outlier, to treat empty fields as outliers The default reporting of blank outlier test vals is now as non-outliers. Use this option to report as outliers. Added for the mighty P Taylor.
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.
12 Jul 2021, RW Cox, Clusterize, level 1 (MICRO), type 6 (ENHANCE) Make min cluster size = 1 (from 2) for DR Glen.
09 Jul 2021, P Taylor, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT) New: '-aff_move_opt ..' to use more than just giant_move in aff step. Also bug fix for when no followers were entered.
30 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Tweak column names *again*. Add in extra check that 3D vols are specified (e.g., with selectors).
29 Jun 2021, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT) -log2 and -log10 options To convert statistics to minus the logarithm of p-value.
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? 28 Jun 2021, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE) Add Linear back to Alpha fading, as well as default Quadratic Drive-able. Menu item under 'Thr' popup. 28 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Reformat report*.1D tables a bit: match key and col names. Also, improve/simplify/clarify names of cols. Thanks, Adam Messinger. 28 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Well, OK, not *really* a new opt---new values accepted for existing opt. The '-olay_alpha ..' can now take Linear or Quadratic (grazie, Bob).
25 Jun 2021, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) add -rand_post_elist_partition This will partition an already defined stim class into new ones. Added on the authority of S Haller.
24 Jun 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL) Add tracking thru optimization of original points That is, with -verb, print out the original index [o=X] as the stages of optimization proceed. This helps determine if the larger number of initial coarse trial candidates parameter sets actually produces viable contenders for the championship. 24 Jun 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 0 (GENERAL) Silence 3drefit warns if changing space of dsets (might confuse users). Unnecessary warning for these temp dsets within the script.
23 Jun 2021, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY) Add the setjmp/longjmp escape mechanism to plusminus warping To gracefully end the program if the OpenMP race condition arises.
22 Jun 2021, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX) calm those grumpy compilers Issues noted by P Taylor. 22 Jun 2021, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY) without -datum, the output now depends on the map func, not the BRIK Done to appease the mysterious D Glen. 22 Jun 2021, P Taylor, SurfLayers, level 2 (MINOR), type 0 (GENERAL) Capture verbose output from ConvertSurface. Also add -no_clean opt. 22 Jun 2021, P Taylor, 3dNwarpCalc, level 2 (MINOR), type 0 (GENERAL) Put in std includes to be able to build on Mac with Clang. Though this program isn't even built...
21 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 5 (MODIFY) Change default blok type and radius for the lpc/lpa methods Old default was -blok 'RHDD(6.54321)'. New default is -blok 'TOHD(0)' where the 0 radius means to compute the blok radius so as to give the blok a volume of 555 times the volume of a base dataset voxel. For 1x1x1 voxels, such as the MNI template, this results in 'TOHD(5.18)'. If users want the old setup, they'll have to use the old blok definition explicitly.
18 Jun 2021, P Taylor, @Install_SURFLAYERS_DEMO1, level 2 (MINOR), type 0 (GENERAL) Created by Sam Torrisi. Help added, temp placeholder data now in place. Will add full demo data soon... 18 Jun 2021, P Taylor, @Install_AP_MULTI_DEMO1, level 2 (MINOR), type 0 (GENERAL) Adding install script for afni_proc.py multi-echo FMRI demo (OHBM, 2021). Demo authors: RC Reynolds, SJ Gotts, AW Gilmore, DR Glen, PA Taylor.
15 Jun 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_imit2w_from_t1w, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_decmap, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_convert_dcm_anat, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, ap_run_simple_rest.tcsh, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Awarp, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @simulate_motion, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 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. 15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @parse_name, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @parse_afni_name, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @move.to.series.dirs, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_in2out, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_erosion_thick, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_bb_thick, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @global_parse, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @djunct_slice_space, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @djunct_glue_imgs_vert, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @compute_gcor, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @clip_volume, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @clean_help_dir, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @build_afni_Xlib, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni.run.me, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @T1scale, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ScaleVolume, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_Caret, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL) Clean up some spacing; avoid single line 'if' conds; use unaliased rm. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @RetinoProc, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Reorder, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ROI_decluster, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Install_InstaCorr_Demo, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Install_ClustScat_Demo, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @GradFlipTest, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ExamineGenFeatDists, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Atlasize, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @2dwarper.Allin, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @1dDiffMag, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions.
14 Jun 2021, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 4 (BUG_FIX) turn of 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.
10 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) rename src/suma_suma.h to src/SUMA/SUMA_X_objs.h This is to avoid glorious case-insensitive name conflicts on Macs. As suggested by the merciful D Glen. 10 Jun 2021, RC Reynolds, SurfLocalstat, level 2 (MINOR), type 1 (NEW_PROG) add Ziad's program to the default build This is to allow use of the 'mode' stat. 10 Jun 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) New opt '-echo', for odd-behavior-on-other-systems-investigtion-purposes. Also print AFNI and program version numbers at top.
09 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 6 (ENHANCE) Changes to make T1-T1 alignment with lpa+ZZ more reliable Problem - aligning whole head volume to MNI template (top of head only) - alignment sometimes fails badly. This problem is much less common if source and base image coverage are compatible. If users will not zero out or chop off the sub-brainstem part of the head, then the following changes made to 3dAllineate will help: a) carry out a larger search in the coarse pass (more trials) b) eliminate 'ov' and 'mi' from lpa+ as these caused problems NOTE: 'ov' and 'mi' are still in lpc+ Also investigated why linux and macos results differ. Tracking optimizer leads to hypothesis that differences in roundoff error slowly accumulate, and then at some point powell_newuoa makes a step decision that can alter the optimizing trajectory significantly. There doesn't seem to be a good way to avoid this. However, with the chanes above, both macos and linux versions work reasonably well, and differ at most in about 2 mm (and that only in one case out of 38 whole head tests). 09 Jun 2021, RW Cox, 3dUndump, level 1 (MICRO), type 2 (NEW_OPT) Add -allow_NaN option To allow some DERANGED AFNI user whose name will not be mentioned to create a dataset containing NaN (Not A Number) floating point values.
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
03 Jun 2021, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 6 (ENHANCE) sync crorden/dcm2niix_console with repo, version v1.0.20210317 Thanks to C Rorden for suggesting the update.
02 Jun 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL) Undo previous tweak to auto_warp.py; back to using *.nii. Reverting, because AFNI_COMPRESSOR has been updated. 02 Jun 2021, P Taylor, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) Undo previous tweak to db_mod.py (for auto_warp.py); back to using *.nii. Reverting, because AFNI_COMPRESSOR has been updated.
01 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) AFNI_COMPRESSOR no longer affects NIFTI (seems AFNI_AUTOGZIP never did)
30 May 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL) Use *.nii.gz, not *.nii, because of current AFNI_COMPRESSOR = GZIP. With current AFNI_COMPRESSOR = GZIP, get problems; now, no more. 30 May 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) New opt '-use_gz' to output gzipped NIFTI even with '-suffix ..'. Part of updating auto_warp.py to use *.nii.gz, not *.nii. 30 May 2021, P Taylor, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) Tweak db_mod.py: prep for auto_warp.py to now always use *.nii.gz. Just mv *.nii.gz files, rather than *.nii, from auto_warp output dir.
29 May 2021, RC Reynolds, SurfLocalstat, level 1 (MICRO), type 2 (NEW_OPT) add 'mode' stat modal smoothing
24 May 2021, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Several small updates for convenience and organization: help updated... more QC images; split intermediate text desc; new cmd_log.
20 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Clean up exiting from help and version checking. Doesn't go via the verbose GOOD_EXIT route anymore, which it shouldn't.
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)
17 May 2021, DR Glen, lesion_align, level 3 (MAJOR), type 1 (NEW_PROG) Alignment for data with large lesions Developed for hemispherectomy and lobectomy data. May be applicable to stroke and smaller lesion data too
12 May 2021, P Taylor, @SUMA_Make_Spec_FS, level 1 (MICRO), type 0 (GENERAL) Remove old/unnecessary comment from help of -NIFTI opt. Referred to earlier misconcept (need even mat dims for anatomical dset).
11 May 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) 1dplot.py improved for backward compatability to Python 2.7. So, for task FMRI, individual stim label plots work again in Py2.7. 11 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Set env var to turn off NIFTI warnings. That is, AFNI_NIFTI_TYPE_WARN -> NO. 11 May 2021, P Taylor, 1dplot.py, level 1 (MICRO), type 0 (GENERAL) Replace str.isnumeric() with str.isdigit(), for backward compatability. Python 2.7 didn't have that method for str type.
10 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 2 (NEW_OPT) New opt: '-set_xhair_gap ..', to allow setting crosshair gap. Default value is -1.
06 May 2021, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE) Make -zskip work with -paired Rejecting any value pairs where either setA or setB is 0.
03 May 2021, P Taylor, 3dClusterize, level 1 (MICRO), type 0 (GENERAL) Add bracket to meta-text above table in case of abs value in table. Thanks, watchful AFNI user YurBoiRene.
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 2 (NEW_OPT) Forgot to actually add in the new opt for data scaling in last change... Now opt '-abs_table_data' is in the code. 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.
23 Apr 2021, P Taylor, 1dplot.py, level 2 (MINOR), type 2 (NEW_OPT) Can force ylabels to wrap at a certain num of chars (-ylabels_maxlen ..). For APQC, so long stimulus labels don't run into each other. 23 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) 1dplot.py improved, so stimulus labels on y-axis will wrap. Reduce/remove overlap of long stim labels.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 7 (REMOVE) This program has been superceded by: adjunct_apqc_tsnr_general. The new version is more... general. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 7 (REMOVE) This program has been superceded by: adjunct_apqc_tsnr_general. The new version is more... general. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 2 (NEW_OPT) More options from @chauffeur_afni here. Tryin' to make nicer images. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 1 (NEW_PROG) Made to replace adjunct_apqc_tsnr_with_mask and adjunct_apqc_tsnr_no_mask. Also expands/generalizes this functionality. 16 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Use newer adjunct_apqc_tsnr_general for TSNR images. Single/more adjunct general prog than previous separate ones. 16 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Internal logic for making TSNR dsets tweaked. TSNR images in QC*/media/ dir get unique name, too (no change for user). 16 Apr 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) New keyword EMPTY for '-topval ..' opt, make scripting easier. Corrected discrete cbar help example, too.
06 Apr 2021, RC Reynolds, ap_run_simple_rest.tcsh, level 3 (MAJOR), type 1 (NEW_PROG) run a quick afni_proc.py resting state analysis for QC
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, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT) -FWHMxyz allows different blurring amounts in different directions 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. 24 Mar 2021, P Taylor, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) New opt: -is_atlas_or_labeltable. 1 if dset has an atlas or labeltable; otherwise, 0.
23 Mar 2021, P Taylor, 3dBrickStat, level 1 (MICRO), type 0 (GENERAL) Uniformize internal spacing. Should be no change in behavior. Just a few comments stretch far still.
16 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) simplify logic in THD_mask_erode(), with negligible slowdown 16 Mar 2021, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally. 16 Mar 2021, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally. 16 Mar 2021, P Taylor, @djunct_4d_imager, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally.
15 Mar 2021, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT) Add -wprefix option This option will write out the computed warp for each sub-brick. Mostly for Zhark's curiousity. 15 Mar 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 5 (MODIFY) Move help from main() to function Allin_Help() 15 Mar 2021, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT) add convenience options -perclist and -perc_quiet
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. 13 Mar 2021, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) distribute libXp.6.dylib, since XQuartz has stopped doing it Thanks to C Gaillard and others on the MB.
10 Mar 2021, RC Reynolds, lib_tsv.py, level 2 (MINOR), type 1 (NEW_PROG) new TSV class library, geared toward BIDS event files 10 Mar 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 2 (NEW_OPT) Add in more control features, so can apply in more cases. Basically just allowing more chauffeur control.
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. 08 Mar 2021, P Taylor, map_TrackID, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3ddot_beta, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dZipperZapper, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dTrackID, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dReHo, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dRSFC, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dROIMaker, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dNetCorr, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dMatch, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dLombScargle, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dDWUncert, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dAmpToRSFC, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller.
06 Mar 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. 06 Mar 2021, P Taylor, @fat_tract_colorize, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. And tweak help to be more useful. 06 Mar 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. 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
05 Mar 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_cormat_warnings_full This version includes the baseline terms in the warning list. 05 Mar 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Have APQC copy the ss_review_basic text file into the QC dir. Might want this text info available for easy parsing at group level.
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, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY) update dotfiles for 'complete' files before running apsearch Do this so apsearch will not tell users to update the dotfiles again. Thanks to D Glen. 03 Mar 2021, RC Reynolds, @clean_help_dir, level 2 (MINOR), type 5 (MODIFY) warn on any error in 'cat *.complete* > xx' commands In MacOS 11 Rosetta terminals, those commands are *sometimes* crashing. Warn on any such failure. Such a crash could cause trouble for other programs, too. Thanks to D Glen. 03 Mar 2021, P Taylor, gen_ss_review_scripts.py, level 2 (MINOR), type 0 (GENERAL) Add sswarper2 to name of recognized progs for getting template dset. Can get uvar for APQC for this top secret NL alignment prog. 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. 03 Mar 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) Make nice new WB mask, make some QC images of mask/segs/ROIs. Also make tables of ROI info (size stuff).
01 Mar 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Fix output dir of an intermediate QC image. The init*uaff* should now be in the usual QC/ dir.
27 Feb 2021, DR Glen, clang macos 11 M1-ARM mods, level 3 (MAJOR), type 0 (GENERAL) Makefile changes for ARM builds for new Macs Makefile, misc. changes for building for M1 27 Feb 2021, DR Glen, gap setting via plugout_drive, level 1 (MICRO), type 2 (NEW_OPT) Set the AFNI GUI crosshair gap with plugout_drive See README.driver for details 27 Feb 2021, DR Glen, atlas labels - remove trailing spaces, level 1 (MICRO), type 4 (BUG_FIX) Remove trailing spaces introduced by @Atlasize
25 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) With non-nonlinear warps, processing now goes all they way through. Bit more *.txt output, fixed mapping of anat follower non-ROI dset.
24 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add options -regress_extra_ortvec, -regress_extra_ortvec_labels Pass sets of regressors of no interest, to go into the baseline. Requested by multiple people, including Carolin31 on MB. 24 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Add more TSNR plotting: if vreg TSNR is calc'ed, or if no mask exists. Also a bug fix in HAVE_MASK definition; fix ranges in some plots. 24 Feb 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 1 (NEW_PROG) Now used in APQC to make TSNR plot. Has mostly required olay/ulay args, for when *no* mask exists.
23 Feb 2021, RW Cox, lots of them, level 1 (MICRO), type 0 (GENERAL) Changes to avoid compile warnings with -Wall option Mostly cosmetic fixes, but a few minor errors discovered and patched. About 50 .c files affected.
22 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) masking is no longer applied to TSNR dset; pass mask_dset to gen_ss Requested by P Taylor. 22 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) New part of regr block: TSNR plot. Shows brain slices. 22 Feb 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 1 (NEW_PROG) Now used in APQC to make TSNR plot. Has mostly required olay/ulay args, as well as mask. 22 Feb 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt: -pbar_comm_gen, for APQC. Also remove warning about ffmpeg unless using MPEG.
21 Feb 2021, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY) remove actual targets in RM for LIBMRI_* 21 Feb 2021, RC Reynolds, @djunct_glue_imgs_vert, level 1 (MICRO), type 5 (MODIFY) allow -help without deps, so move dependency tests
19 Feb 2021, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY) updates for ShowMode in SUMA_xColBar.c Resolve compiler warnings, but avoid logic changes at the same time as XQuartz beta issues. So temporarily keep original logic. Once we feel stable with XQuartz, look into expected fixes. Search for 'todo: apply ShowMode' in SUMA_xColBar.c.
18 Feb 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) warn about problematic version of XQuartz Bad versions seem to be 2.8.0_alpa*, 2.8.0_betas[12] (3+ okay?). With improvements we have seen, maybe we should warn on any beta.
17 Feb 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) moved AFNI_ijk_* protos from afni.h to 3ddata.h All thd_coords.c protos are in 3ddata.h now.
10 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL) More QC images: WM and GM tissue, solo. Thanks for suggestions, P Molfese. 10 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Add in -mask_ss option, to replace skullstripping with a mask. For example, using fs*mask*nii from @SUMA_Make_Spec_FS after FS.
09 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 0 (GENERAL) Add fractional volume info to the text file. This makes 2 new columns in the output *.1D files. 09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL) New column of ROI vol fraction, relative to fs_parc_wb_mask.nii.gz. This prog should always be run after adjunct_suma_fs_mask_and_qc. 09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL) Renamed, from adjunct_suma_rois_qc.tcsh. Removing extension. 09 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 0 (GENERAL) Make new mask dset from parcellation. Add new image of new dset. 09 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL) Renamed, from adjunct_suma_fs_qc.tcsh. Removing extension.
08 Feb 2021, RW Cox, AFNI gui, level 1 (MICRO), type 6 (ENHANCE) Add Mean/Sigma statistic to Button 3 popup in graph viewer Kind of a cheap TSNR check for raw data. 08 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG) Will add to @SUMA_Make_Spec_FS for automatic QC output. This makes *.1D files of voxel counts of parcellations and segs. 08 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG) Will add to @SUMA_Make_Spec_FS for automatic QC output. This makes images of the brain mask, tissue segs and parcellation.
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
05 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Add in more intermediate QC snapshots (intermed align): init*jpg Also add '-echo' opt for verbose terminal stuff.
03 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New QC image, of affine warping. Also pass along '-echo' opt to modal smoo/report script.
27 Jan 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE) Enhance -PearSave option Now it works with -allcostX to give the LPC values at the start of the run, instead of only at the end. Now it works with any cost functional, say '-hel', instead of '-lpc' and '-lpa'. That is, you can get the local Pearson stuff even if it isn't actually used in the optimization. 27 Jan 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) New run script created (run_01*) in L_MAKE_DRIVE_SCRIPT block. Opens std.141*both*spec in SUMA and SurfVol in AFNI, and starts talking. 27 Jan 2021, P Taylor, 3dAttribute, level 2 (MINOR), type 0 (GENERAL) Update help to have fancy sections and more examples. Also provide link to README.attributes file, for user reference.
26 Jan 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 2 (NEW_OPT) New -PearSave option Saves the local Pearson correlations into a dataset at the end of an alignment. Mostly for visualization fun. 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.
11 Jan 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) AFNI graph viewer box labels now selectable from menu In the Colors, Etc. menu, new items were added to enable and control the labels used in Box mode. Keystroke ctrl-B cycles between all Data modes. In addition, labels can now be drawn for graph matrix size up to 9x9.
03 Jan 2021, RC Reynolds, SurfMeasures, level 2 (MINOR), type 5 (MODIFY) shift memory allocation/free around, mostly to match libSUMA Inspired by C Rorden via sanitizer warnings.
31 Dec 2020, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) modify help: be more clear about bandpassing being undesirable Also, add example of high-pass filter to model slow drift. See help for option -regress_polort.
29 Dec 2020, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with nifti_clib 29 Dec 2020, RC Reynolds, nifti_tool, level 1 (MICRO), type 6 (ENHANCE) add help example for creating a new dataset given a raw data file
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, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New default feature_size: 0.5. (Old default: was unset). Made almost no dif in mac demo, but should be slightly more robust, in gen . 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. 21 Dec 2020, P Taylor, 3dROIMaker, level 1 (MICRO), type 0 (GENERAL) Tweak internal handling of reading inputs, prohibit hanging args. Now, hanging args should produce error (not just be silently ignored). 21 Dec 2020, P Taylor, 3dClusterize, level 1 (MICRO), type 0 (GENERAL) Tweak internal handling of reading inputs, prohibit hanging args. Now, hanging args should produce error (not just be silently ignored).
17 Dec 2020, RC Reynolds, 1dBport, level 1 (MICRO), type 4 (BUG_FIX) guard against silent failure of int overflow for ftop
01 Dec 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Tweaked default temp 'junk' filename to avoid low-probability badness New opt '-tmp_name_nice' for, well, read opt name. Improved help, too.
12 Nov 2020, P Taylor, fat_proc_connec_vis, level 1 (MICRO), type 0 (GENERAL) Set some env vars at top of script to turn off compression. Was causing odd error in one case.
06 Nov 2020, P Taylor, adjunct_tort_read_dp_align.py, level 2 (MINOR), type 1 (NEW_PROG) Script to read TORTOISE-DIFFPREP *_transformations.txt files. Puts them into usable order for calc'ing enorm and plotting mot/pars. 06 Nov 2020, P Taylor, adjunct_tort_plot_dp_align, level 2 (MINOR), type 1 (NEW_PROG) Script (tcsh) to translate TORTOISE-DIFFPREP *_transformations.txt files Wraps new adjunct_tort_read_dp_align.py and 1dplot* to make plots.
02 Nov 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Can now output SVG files, and can use newline chars in labels. Had to deal with newline escape seq internally.
28 Oct 2020, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL) Extra QC image: initial overlap of source and base dsets. Should help to know, in case anything goes awry later. 28 Oct 2020, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL) Extra QC image: initial overlap of T1w and T2w dsets. Should help to know, in case anything goes awry later.
19 Oct 2020, P Taylor, @djunct_overlap_check, level 3 (MAJOR), type 1 (NEW_PROG) Make of overlap of 2 datasets (esp for pre-align check, AW or SSW). Will make both non-obl and 3dWarp-deob'ed images of olap (and report). 19 Oct 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Simplifying output dir: Phase II and III. Thanks again, B Jung! New intermediate dir, animal_outs update, helpfile rewritten. 19 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Added new QC image to QC/ dir: initial source-base alignment. If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report. 19 Oct 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Added new QC image: initial source-base alignment (@djunct_overlap_check) If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report.
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Simplifying output dir: Phase I. Thanks, Ben Jung, for good suggestions! Put report*1D in QC/, and do*.tcsh and surfaces_* in new surfaces/ dir. 16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Add in status checks after many afni progs, to exit at/near first failure. Should be no change in output for users (in successful runs). 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.
29 Sep 2020, RC Reynolds, 3dANOVA3, level 1 (MICRO), type 6 (ENHANCE) be specific about limits for 'param must be in' error messages
24 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Put in status checks through script to exit with error if any step fails. Should provide nicer behavior if something gang agley.
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.
15 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) whine if .zshrc references all_progs.COMP.bash; backup for distro
14 Sep 2020, RC Reynolds, apsearch, level 2 (MINOR), type 6 (ENHANCE) create complete.zsh files - like bash ones, but cleaned a little 14 Sep 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) update .zshrc: set PATH and DYLD_L_P..., and source all_progs.COMP.zsh
10 Sep 2020, DR Glen, Driving AFNI to get values, level 2 (MINOR), type 6 (ENHANCE) Drive AFNI to get current value in OLay, Threshold or ULay+ Can also get ULay and OLay prefixes
02 Sep 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) add options -show_field and -show_field_names Using the new -show_field option, for each entry one can show: - the full entry (as before) - only the first/main line - only the program name, or date, or author, etc. 02 Sep 2020, P Taylor, @SkullStrip_TouchUp, level 2 (MINOR), type 0 (GENERAL) Replace '-e' at top with several later status checks; 'exit 0' after help. No effect on output, except being more general.
01 Sep 2020, P Taylor, fat_roi_row.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_proc_grad_plot, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution. Already have a better one (with fewer dependencies!) ready to go. 01 Sep 2020, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mvm_review.py, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution. This program never even made it to full beta status. 01 Sep 2020, P Taylor, fat_mvm_prep.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mvm_gridconv.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_lat_csv.py, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution, with lib: lib_fat_Rfactor.py. R deps are a mess between Py2 and Py3; might rewrite better in future. 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.
31 Aug 2020, RC Reynolds, afni_python_wrapper.py, level 1 (MICRO), type 2 (NEW_OPT) add -joinn for list output; add list_intersect and list_diff funcs
27 Aug 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 1 (MICRO), type 6 (ENHANCE) set up for alternatively building without SUMA 27 Aug 2020, RC Reynolds, @diff.tree, level 1 (MICRO), type 4 (BUG_FIX) better handling of missing trailing directory args 27 Aug 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 5 (MODIFY) Well, usage+output shouldn't really change, but it should be more stable. There is also a new opt: -align_centers_meth (read the help).
26 Aug 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 6 (ENHANCE) much limiting of line lengths to 80 chars - should be no real change 26 Aug 2020, RC Reynolds, ClustExp_StatParse.py, level 1 (MICRO), type 6 (ENHANCE) python 3 update to decode() subprocess output 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.
25 Aug 2020, RC Reynolds, sqwave, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, siemens_vision, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, plug_3ddup.so, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, mritopgm, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, mayo_analyze, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use nifti_tool 25 Aug 2020, RC Reynolds, lpc_align.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, ge_header, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, ftosh, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, ent16, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, check_dset_for_fs.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use afni_proc.py 25 Aug 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added new types TYPE_REMOVE and TYPE_REINSTATE This is to track when programs or notable functionality gets removed. 25 Aug 2020, RC Reynolds, abut, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Xphace, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Ifile, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, FD2, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use afni 25 Aug 2020, RC Reynolds, DoPerRoi.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Dimon1, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, AlphaSim, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dClustSim 25 Aug 2020, RC Reynolds, @snapshot_volreg3, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use @snapshot_volreg 25 Aug 2020, RC Reynolds, @make_stim_file, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use timing_tool.py 25 Aug 2020, RC Reynolds, @auto_align, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, @UpdateAfni, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use @update.afni_binaries 25 Aug 2020, RC Reynolds, @DTI_studio_reposition, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dttest, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dttest++ 25 Aug 2020, RC Reynolds, 3dproject, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dnoise, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dfim, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dDeconvolve 25 Aug 2020, RC Reynolds, 3ddup, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dbuc2fim, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dWavelets, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dUniformize, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dUnifize 25 Aug 2020, RC Reynolds, 3dProbTrackID, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dTrackID 25 Aug 2020, RC Reynolds, 3dMax, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dBrickStat 25 Aug 2020, RC Reynolds, 3dICC_REML.R, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dFourier, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dBandpass 25 Aug 2020, RC Reynolds, 3dFWHM, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dFWHMx 25 Aug 2020, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dDeconvolve 25 Aug 2020, RC Reynolds, 3dCountSpikes, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dToutcount 25 Aug 2020, RC Reynolds, 3dAnatNudge, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, 3dAOV.R, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dANALYZEtoAFNI, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dcopy or to3d 25 Aug 2020, RC Reynolds, 1dDW_Grad_o_Mat, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 1dDW_Grad_o_Mat++
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.
09 Aug 2020, DR Glen, @ROI_decluster, level 2 (MINOR), type 1 (NEW_PROG) Remove small clusters or single voxels in datasets with many ROIs Keeps only the largest part(s) of the ROI with adjustable threshold. Used for datasets with many ROIs, like those found in an atlas. Can be used in combination with @ROI_modal_grow
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, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 1 (NEW_PROG) Install MACAQUE_DEMO_REST_1.0, for macaque resting state FMRI examples. Has a '-lite_version' opt for truncated EPI version, smaller download. 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.
30 Jul 2020, P Taylor, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 0 (GENERAL) Now install MACAQUE_DEMO_2.1, which should be the new normal. Script checks for things on install, makes recs, more full demo. 30 Jul 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Make easier to find template in case data has moved around. Also use wildcard to clean intermed file, in case auto GZIP is on. 30 Jul 2020, DR Glen, vol2surf nzmode, level 2 (MINOR), type 2 (NEW_OPT) nonzero mode option for 3dVol2surf and vol2surf plugin Computes most common non-zero value along segment 30 Jul 2020, DR Glen, @ROI_modal_grow, level 2 (MINOR), type 1 (NEW_PROG) Grow ROIs using nonzero mode in 1 voxel neighborhood increments Similar functionality as in 3dROImaker but uses non-zero mode to grow sets of regions, like those found in an atlas
28 Jul 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) add initial afni_history_laurenpd.c
21 Jul 2020, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 6 (ENHANCE) add env var control over pre-comp e2x, limit and pieces See AFNI_MODEL_PRF_PRECOMPUTE_EX, AFNI_MODEL_PRF_MAX_EXP and AFNI_MODEL_PRF_MAX_EXP_PIECES. 21 Jul 2020, RC Reynolds, get_afni_model_PRF_6, level 2 (MINOR), type 6 (ENHANCE) add initial NT parameter
16 Jul 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update for shared libmri.so: linux_centos_7_64, linux_ubuntu_16_64
15 Jul 2020, P Taylor, 3ddot_beta, level 2 (MINOR), type 0 (GENERAL) Moved header dep of suma_suma.h -> suma_objs.h. Should be no output change. 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). 15 Jul 2020, P Taylor, 3dTrackID, level 2 (MINOR), type 0 (GENERAL) Moved header dep of suma_suma.h -> suma_objs.h. Should be no output change. 15 Jul 2020, P Taylor, 3dTORTOISEtoHere, level 2 (MINOR), type 0 (GENERAL) Moved header dep of suma_suma.h -> suma_objs.h. Should be no output change. 15 Jul 2020, P Taylor, 3dNetCorr, level 2 (MINOR), type 0 (GENERAL) Moved header dep of suma_suma.h -> suma_objs.h. Should be no output change. 15 Jul 2020, P Taylor, 3dEigsToDT, level 2 (MINOR), type 0 (GENERAL) Moved header dep of suma_suma.h -> suma_objs.h. Should be no output change. 15 Jul 2020, P Taylor, 3dDTtoNoisyDWI, level 2 (MINOR), type 0 (GENERAL) New opt for controlling random seed is available (for testing). Also, moved dep of suma_suma.h -> suma_objs.h (shd be no output change).
12 Jul 2020, DR Glen, atlas longnames change, level 1 (MICRO), type 5 (MODIFY) atlas longnames and labeling change atlas labels and labeltable labels are not both printed if same atlas labels and longnames not both printed if same 3dROIstats only shows regular labels now, no longname atlas labels
01 Jul 2020, P Taylor, @Install_NMT, level 3 (MAJOR), type 1 (NEW_PROG) Installer for the NIMH Macaque Template(s) v2, and the CHARM (atlases). Courtesy of Ben Jung, Adam Messinger, et al.
23 Jun 2020, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) Add support for *.tsv and *.csv files Tab and Comma separated value files will be read in, like 1D files, and can be selected by a chooser, including in a plugin.
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.
19 Jun 2020, RC Reynolds, parse_fs_lt_log.py, level 1 (MICRO), type 6 (ENHANCE) update for python3, though this program might not be in use 19 Jun 2020, RC Reynolds, afni_restproc.py, level 1 (MICRO), type 5 (MODIFY) update for python3; add extra suggests that it is obsolete
17 Jun 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 2 (NEW_OPT) Add legend functionality, along with opts for label and loc specifying. New opts: -legend_on, -legend_labels, -legend_locs. 17 Jun 2020, P Taylor, 1dplot.py, level 1 (MICRO), type 0 (GENERAL) Add -hview functionality. Where has this been all my life??
14 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) For vstat with seedbased corr (rest), use 0.3 as thr value of corr map. Returning value to what it had been for a long time, based on examples.
11 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add Stride to graphing (every n-th time point, n=1..9)
10 Jun 2020, P Taylor, convert_cdiflist_to_grads.py, level 3 (MAJOR), type 1 (NEW_PROG) For GE scanners, we might want a cdiflist* file for DWI grad info. This prog converts such beasts into usable grad/bvalue files for proc.
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*.
04 Jun 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 0 (GENERAL) Improve couple things in help file; change def cbar. More useful 'divergent' class of cbar as default. 04 Jun 2020, DR Glen, align_epi_anat.py epi stripping options, level 1 (MICRO), type 2 (NEW_OPT) epistrip_opts/dset2strip_opts
03 Jun 2020, P Taylor, lib_mat2d_plot.py, level 3 (MAJOR), type 0 (GENERAL) Many updates to functioning, defaults, reading argv, applying user opts. Help file added as well; works with main proc: fat_mat2d_plot.py. 03 Jun 2020, P Taylor, fat_mat2d_plot.py, level 3 (MAJOR), type 1 (NEW_PROG) FINALLY, a python3 program to plot 3dTrackID and 3dNetCorr output. Plots *.grid and *.netcc files; replaces fat_mat_sel.py. 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.
02 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add PM (plus/minus) curve plotting options Added to the 'Colors Etc' menu. Curves, Bars, and Fill.
01 Jun 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) in populate_nifti_image(), call time series only if ntt>1 or NVALS==1 This is to avoid confusion when a time series is used to master a non-time series dataset. 01 Jun 2020, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_regs and -show_regs_style Show column indices or labels of an xmat.1D file with empty (all-zero) regressors. An index list can be space or comma-separeated, or encoded. Example 30 shows typical use cases. Added for S Haller. 01 Jun 2020, RC Reynolds, 3dAllinate, level 1 (MICRO), type 5 (MODIFY) clear any initial ntt from master 01 Jun 2020, P Taylor, lib_mat2d_base.py, level 2 (MINOR), type 0 (GENERAL) Migrated from lib_mat2d.py; tweaks added. Add in few more mat2d attributes; rearrange methods. 01 Jun 2020, P Taylor, lib_mat2d.py, level 2 (MINOR), type 0 (GENERAL) Start some new functionality for 2D matrices. In particular, these are for 3dTrackID and 3dNetCorr output. 01 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) For vstat with seedbased corr (rest), use 0.2 as thr value of corr map. The value 0.3 seemed pretty high (esp. if no smoothing is applied). 01 Jun 2020, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL) Add new funcs for convenient message printing, in the AFNI style. IP(), EP() and WP(), which are wrappers to use APRINT(). 01 Jun 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Reformat report*.1D tables a bit. Add in a KEY; change U/W to A/B; minor format stuff.
31 May 2020, RC Reynolds, @diff.files, level 1 (MICRO), type 2 (NEW_OPT) add -verb 31 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Change range of grayscale when EPI is ulay (ve2a and LR flipcheck). Now 2-98percent (nonzero). 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.
30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 1 (NEW_PROG) Perform modal smoothing, and go back and add in any ROIs that were lost. May be useful in @animal_warper; may be good to add mask stuff, too. 30 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Default modal smoothing now is with replacement of any lost ROIs. Uses @djunct_modal* script; opt to not replace. More QC images now, too. 30 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) String selector of lost ROIs now is only comma-separated list. Discovered couldn't have both comma- and '..'-separated list in selector. 30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 0 (GENERAL) Now use *.nii.gz files for all intermeds, not *.nii. Works better with @animal_warper this way. 30 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Apply input_abbrev earlier in processing. Homogenize naming, I think, if it is being selected.
28 May 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add curve smoothing plot to graph viewer Invoked from 'Colors Etc' menu, or by pressing the 's' key. [For GC] 28 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Now report DF information in vstat block. Needed to be able to interpret F-stat and t-stat values.
26 May 2020, RC Reynolds, @move.to.series.dirs, level 1 (MICRO), type 5 (MODIFY) call afni_python_wrapper.py instead of old afni_util.py 26 May 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Two major changes in output: ve2a and LR-flipcheck now have EPI as ulay. Most anats are SSed, so better edges? Thanks for suggestion, O Esteban! 26 May 2020, P Taylor, @djunct_edgy_align_check, level 3 (MAJOR), type 0 (GENERAL) Several changes to make this appropriate using EPI as ulay. New opts, couple small bug fixes, couple tweaks. 26 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Now output an AFNI-style string selector of 'lost' ROI values. This might make it easier to see the diffs the volumes.
25 May 2020, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) add libexpat.1.dylib to EXTRA_INSTALL_FILES R was upgraded to 3.6 (on the 10.12 build machine), since that is the current G Chen version requirement, making R_io.so work for people with only 3.6. But libexpat was upgraded too, which afni depends on, meaning systems needed that new version of libexpat, or afni would not work. Instead, libexpat.1.dylib is now simply included with the binaries. Thanks to S Gotts and K Tran for reporting the problem.
22 May 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Change this prog to do all work in a workdir that can be cleaned. Should not have any effect on the usage or outputs.
21 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT) add options -NN1, -NN2 and -NN3 Also, fix tiny origin shift when large zero-padding is applied. 21 May 2020, P Taylor, afni_seeds_per_space.txt, level 3 (MAJOR), type 0 (GENERAL) Keep up with change of macaque standard space naming: stereoNMT -> NMT2. 'stereoNMT' is an ex-parrot. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 3 (MAJOR), type 1 (NEW_PROG) Adjunct program for @animal_warper.py; build ROI report table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Add reports of warped and unwarped ROIs, via adjunct_aw_tableize*.py. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Require mode_smooth_size as input, and include it in table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Report now reports mode_smooth_size. Thanks to D Glen and A Messinger for helpful feedback+inputs.
20 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update THD_mask_erode_sym() akin to take NN param This matches the dglen update to THD_mask_dilate(). 20 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX) fix history and memory loss
19 May 2020, DR Glen, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) nzvolume - volume of nonzero voxels 19 May 2020, DR Glen, 3dBrickStat, level 1 (MICRO), type 4 (BUG_FIX) Volume - absolute value of voxel dimensions used now
18 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Large number of under-the-hood changes, as well as new opts. More general handling of followers and choosing file abbrevs. 18 May 2020, P Taylor, afni_seeds_per_space.txt, level 2 (MINOR), type 0 (GENERAL) Updated APQC seed locations for stereoNMT space. More centralized now in GM and in specific ROIs; aud away from vessel.
14 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Large number of under-the-hood changes, for readability/clarity. Change echo->printf, spacing, clear comments, etc. No output changes.
12 May 2020, RW Cox, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE) Allow output of .jpg files for 2D images Actually, any AFNI program that writes a 2D 'dataset' will now do so in JPEG format if the prefix ends in '.jpg'. Similarly for '.png' and PNG format. However, note that most programs produce scalar (non-RGB) images, which will thus be monochrome - even if the input is color.
11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update web links to help pages in uber*.py Update uber_align_test.py, uber_skel.py, uber_subj.py and uber_ttest.py. 11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) updates for python3 Update xmat_tool.py, quick.alpha.vals.py, read_matlab_files.py, uber_align_test.py and uber_skel.py.
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, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT) -nosquash, to avoid soft cap on large intensities In other words, to skip the change of 30 Jan 2019, which was causing trouble for someone doing oinker imaging! 04 May 2020, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 6 (ENHANCE) make partual updates for python3 04 May 2020, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY) remove tabs from a bunch of files 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. 04 May 2020, P Taylor, @Install_IBT_DATASETS, level 2 (MINOR), type 1 (NEW_PROG) Installer for the Indian Brain Templates. Enjoy. Courtesy of Dr. Bharath Holla, et al.
30 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 0 (GENERAL) Added YouTube button to afni GUI.
29 Apr 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY) for recur, def to pub/dist/bin/misc; terminate on failed test download 29 Apr 2020, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 6 (ENHANCE) add AFNI_DRIVE_OPTS_XVFB env var for adding opts to Xvfb This will probably be modified later, but it allows one to pass something like '-nolisten inet6' if IPv6 is not working. Thanks to W-L Tseng.
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.
27 Apr 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Added a help example for integrating output into afni_proc.py. ... because otherwise *I* forget how to use the outputs.
24 Apr 2020, P Taylor, 3dLMEr, level 2 (MINOR), type 0 (GENERAL) Updating this R file for GC. So I don't really know what the changes do. ... though I reeeallly want to pretend the changes were mine, ALL MINE. 24 Apr 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL) Sidedness of testing will no longer be checked for non-stat thr vols. It must be Daniel Glen's birthday today (two-sided, non-stat p<0.9999).
23 Apr 2020, RC Reynolds, to3d, level 1 (MICRO), type 4 (BUG_FIX) allow no controller open on input of JPEG image 23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Added new help example. Demonstrates useful colorbar-entry functionality. 23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Use '-colorscale_idx_file ..' to control AFNI env var AFNI_COLORSCALE_xx. Provides a way for user-created cbar info to be input+used.
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.
21 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 2 (NEW_OPT) Added -all_dsets to load all datasets togther.
16 Apr 2020, P Taylor, adjunct_simplify_cost.py, level 1 (MICRO), type 1 (NEW_PROG) Adjunct program for (soon to be updated) @SSwarper. Convert cost name to simpler version, for some application(s). 16 Apr 2020, P Taylor, @djunct_ssw_intermed_edge_imgs, level 1 (MICRO), type 1 (NEW_PROG) Adjunct program for (soon to be updated) @SSwarper. Generates images for intermediate QC/tracking.
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.
10 Apr 2020, RW Cox, AFNI gui, level 2 (MINOR), type 2 (NEW_OPT) Add -norm option for normal font sizes
08 Apr 2020, RW Cox, 1dplot, level 2 (MINOR), type 6 (ENHANCE) Add '0' to the -dashed option -dashed codes are now 1 = solid 2 = longer dashes 3 = shorter dashes 0 = no line, use boxes Code 0 is new, to allow a graph with some data plotted with lines and some without.
07 Apr 2020, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) add -see_also and -ver_man to help create a quick man page To create a man page (via help2man), consider: nifti_tool -see_also > nt.see_also.txt help2man --help-option=-help --version-option=-ver_man \ --include nt.see_also.txt --no-info nifti_tool \ | gzip > nifti_tool_manpage.1.gz after which one can install the file, or test via man ./nifti_tool_manpage.1.gz (see the uncompressed version for syntax).
31 Mar 2020, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 6 (ENHANCE) update for python3 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, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) have module_test_lib.py (and so afni_proc.py) work on python 2.6 again Done for S Horovitz. 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) rigid_equiv - rigid equivalent affine alignment 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX) NIFTI view equivalent for epi2anat alignment fix
27 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY) PY_LIBS 27 Mar 2020, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Rearrange variable/function definitions in afnipy libs (no more interdep). All changes just 'under the hood'---should be no output differences. 27 Mar 2020, P Taylor, apqc_make_html.py, level 1 (MICRO), type 0 (GENERAL) Rearrange variable/function definitions in afnipy libs (no more interdep). All changes just 'under the hood'---should be no output differences. 27 Mar 2020, DR Glen, @animal_warper center_shift, level 2 (MINOR), type 2 (NEW_OPT) Allow for center shifting or not
26 Mar 2020, RC Reynolds, apqc_make_tcsh.py, level 1 (MICRO), type 5 (MODIFY) move ohtml to lib_apqc_tcsh.py and remove import of apqc_make_html This is in keeping with all python libs being under afnipy.
24 Mar 2020, RC Reynolds, python_module_test.py, level 2 (MINOR), type 5 (MODIFY) restore approximate previous behavior
23 Mar 2020, RC Reynolds, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) add options -oblique_recenter and -oblique_recenter_raw Adjust the origin so the cardinalized 0,0,0 (e.g. seen in the afni GUI) is in the same brain location as it was originally (in the scanner?). So when viewing an oblique volume on top of a '3dWarp -deoblique' output, coordinate 0,0,0 will match between them.
20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs 20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs
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
17 Mar 2020, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT) Modify font size options - hopefully easier now 1) Change meaning of 'plus' fonts to be bigger than before. 2) Change so that 'plus' twice on command line equals 'big'. 3) Add simpler options '-big' and '-plus' and '-minus'. Combined, these should make it easier to do font size changes.
12 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) point web help for program to sphinx tree Also, added -hweb/-h_web for python progs that use option_list.py. 12 Mar 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 2 (MINOR), type 1 (NEW_PROG) test for a valid DrawingAreaWidgetClass pointer 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, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) This program has been deemed unnecessary. Thanks for the FS folks for discussions/clarifications on this. 12 Mar 2020, P Taylor, 3dReHo, level 2 (MINOR), type 0 (GENERAL) Alter output format if ROI neighborhood values of ReHo are calc'ed. Make 2 col (ROI val; ReHo val). Output multiple text files, if nec, too. 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.
11 Mar 2020, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE) Add Card or Obliq notice to image viewers 11 Mar 2020, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) add details on why some help examples are not considered complete And corrected status of Example 11, changed to recommended. Thanks to K Knutson for questioning the status. 11 Mar 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Swap ulay/olay in va2t (anat->ulay); clearer image, maybe. Make template (if used) ulay in most other QC blocks.
10 Mar 2020, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE) Add dataset-level weights to 3dttest++ Per the request of users in Tulsa. New options -setweight[AB] allow user to provide weights for the importance of a user in the calculations.
05 Mar 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY) for now, use mris_convert/3dcopy for extra annot files So standard mesh version will not have a proper label table, but the values will be appropriate and more usable in suma. This is done to import the Schaefer/Yeo atlases onto standard meshes. Done with D Glen.
03 Mar 2020, RC Reynolds, 3dttest++, level 1 (MICRO), type 5 (MODIFY) have 3dttest++ -Clustsim fail immediately if -prefix includes a path
27 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -fsannot_ver; apply -extra_annot_labels output as -extra_fs_dsets 27 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) New opt '-warpscale' added; is a new opt in 3dQwarp, can be tweaked here now. Control flexibility of warps. Right now testing different values.
26 Feb 2020, RW Cox, machdep, level 2 (MINOR), type 6 (ENHANCE) First step for allowing floating round randomization Code in machdep.c, enabled by environment variable AFNI_RANDOMIZE_ROUNDING, lets a program invoke macro RAND_ROUND to randomize the IEEE rounding mode. This requires compiling with the flag -DUSE_FENV to enable use of the C99 function fesetround() to set the rounding mode -- see machdep.h. So far, only 3dAllineate has any parts that use RAND_ROUND -- that is, if you set AFNI_RANDOMIZE_ROUNDING to YES and run 3dAllineate, the results will change from a 'normal' run. How much? That's the point of this update, to see how sensitive the output is to the accumulation of tiny changes. 26 Feb 2020, RW Cox, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE) Always check cmass shifts, and provide warnings if not enabled That is, if -cmass is NOT on, but the cmass shifts would be large, put out a WARNING message at the start and at the end. 26 Feb 2020, RC Reynolds, @SUMA_AlignToExperiment, level 1 (MICRO), type 5 (MODIFY) NIFTI fails for -exp_anat, so have it fail early and explain Thanks to D Oswalt for noting the problem. 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. 26 Feb 2020, DR Glen, @animal_warper ROIdset followers, modal smoothing, level 2 (MINOR), type 2 (NEW_OPT) Allow for ROIs to follow into template space and modal smoothing ROIs are transformed with nearest neighbor interpolation Both ROIs and segmentation followers from the template space are now modally smoothed within 3 voxel neighborhoods
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) New min|max range on vox size; update report text. Based on tests with FS data. 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, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add -warpscale option To scale the warp displacments down at each level, for experimentation. 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.)
22 Feb 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Temporary files now have a random string in their prefix. Thus, can have multiple runs in same directory simultaneously sans problem e. 22 Feb 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can control AGIF frame rate, using opt (-agif_delay) to control AFNI env var. Thanks to RCR for pointing out the env var.
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, afni_python_wrapper.py, level 3 (MAJOR), type 1 (NEW_PROG) replaces afni_util.py as a main This program can theortically be used to call any AFNI python function from the shell. 19 Feb 2020, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY) no longer available as a main executable 19 Feb 2020, RC Reynolds, apsearch, level 1 (MICRO), type 5 (MODIFY) get process depth via afni_python_wrapper.py afni_util.py main was moved to afni_python_wrapper.py. 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. 19 Feb 2020, P Taylor, adjunct_select_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_select_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_make_script_and_rst.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_is_label.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_is_label.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_combine_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_calc_mont_dims.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, DoPerRoi.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @DoPerRoi.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) New QC image outputs added. One for skullstripping (orig space) and one for warping (ref space).
18 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) help examples now include some developed outside of afni_proc.py This includes some class demos, along with pamenc and NARPS. Include a line about whether each example is reasonably recommended. Done to appease the mighty P Taylor. 18 Feb 2020, RC Reynolds, @Align_Centers, level 1 (MICRO), type 4 (BUG_FIX) fix copy-and-paste erro and missing endif Thanks to R Kampe for noting the problem.
17 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Reorganized under the hood, deal with censoring in a better way. Easier to tweak/update changes now. 17 Feb 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Opt -censor_hline can now take a keyword NONE as an entry. Useful if looking at multiple inputs and only some have censor lines.
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. 14 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -compare_opts_vs_opts One can compare two afni_proc.py commmands sequentially, that are not part of the stored examples list. Consider: afni_proc.py ... first option set ... \ -compare_opts_vs_opts \ ... second option set ... It is okay for 'second option set' to include the afni_proc.py command name, in case two scripts are concatenated. 14 Feb 2020, DR Glen, @animal_warper dset followers, level 2 (MINOR), type 2 (NEW_OPT) -dset_followers to apply same transformations as dset 14 Feb 2020, DR Glen, @Align_Centers shift xform, level 2 (MINOR), type 2 (NEW_OPT) Move center/origin by known amount from 1D file Large translations in nonlinear warp interpolation can use vast amounts or memory in the 3dNwarpApply implementation. By doing center alignment separately, we can remove the memory and computational costs. The new options are -shift_xform and -shift_xform_inv.
12 Feb 2020, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) add ability to compare against examples Add options -compare_opts, -compare_example_pair, -show_example and -show_example_names. Consider these examples: afni_proc.py -show_example 'Example 11b' afni_proc.py -show_example_names afni_proc.py ... my options here ... -compare_opts 'Example 11' Motivated by C Gaillard and P Taylor. 12 Feb 2020, DR Glen, 3dCM Icent, Dcent, level 2 (MINOR), type 2 (NEW_OPT) alternative centers To force centers to lie within a region -Icent for internal center, -Dcent for distance center
10 Feb 2020, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE) Add reading Apple .heic images (via magick tool)
07 Feb 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) reduce X11 program deps Possibly define LLIBS_X11 in top-level Makefile (as current LLIBS) and then remove X libs from LLIBS. M.INCLUDE will define LLIBS if not set. Move suma_help to IMOBJS. 07 Feb 2020, RC Reynolds, Makefile.linux_fedora_28_shared, level 2 (MINOR), type 6 (ENHANCE) build main non-X11, non-SUMA AFNI program without X deps Set LLIBS_X11 to current LLIBS, and give it to SUMA_LINK_LIB. Remove all X11 libs from LLIBS. Add -DREPLACE_XT to CEXTRA. Note: without REPLACE_XT, LLIBS could still just use Xt and X11. And made the same mods to Makefile.linux_xorg7_64.
05 Feb 2020, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT) Add -LJorder option To order voxels by their Ljung-Box statistics. 05 Feb 2020, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT) list all global options via 'PROG.py -optlist_show_global_opts' Also, add -optlist_show_argv_array to display afni_proc.py options in python dictionary format. This could be done with any OptionList-based python program. 05 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add inital new library for processing example, lib_ap_examples.py
04 Feb 2020, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) add help for a few esoteric options
03 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -extra_annot_labels 03 Feb 2020, RC Reynolds, dicom_hdr, level 1 (MICRO), type 2 (NEW_OPT) add -siemens_csa_data Same as 3 -slice_times_verb opts. 03 Feb 2020, RC Reynolds, Dimon, level 1 (MICRO), type 6 (ENHANCE) show CSA data on high debug 03 Feb 2020, P Taylor, @djunct_anonymize, level 2 (MINOR), type 1 (NEW_PROG) Anonymize files, and maybe add a note. Can either edit input directly, or make a copy + edit that. 03 Feb 2020, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT) Can anonymize output dsets: -anonymize_output. Fairly self-explanatory opt.
02 Feb 2020, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT) Add -qval option to 3dPVAL [for GC]. Merry Groundhog Day!
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. 29 Jan 2020, P Taylor, fat_proc_dwi_to_dt, level 1 (MICRO), type 0 (GENERAL) Try to make a couple output images (dwi*b0*.png) a bit clearer. Make olay use 95%ile value as cbar max, rather than 100%.
27 Jan 2020, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE) add basis=BASIS parameter when defining timing class Done for geenaianni on MB. 27 Jan 2020, RC Reynolds, @diff.tree, level 2 (MINOR), type 2 (NEW_OPT) add -show_list_comp, to do pairwise comparison of file names 27 Jan 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) gzip SUMA/*.nii, except for SurfVol 27 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) Program now outputs QC images automatically. These are output into a PREFIX_QC directory each run. 27 Jan 2020, P Taylor, @SSwarper, level 3 (MAJOR), type 0 (GENERAL) Large set of updates; many new opts added, too; generally much improved warps. Heavily tested on 178 subj across studies; output fnames are same, though. 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 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program now requires specifying a mode for re/defacing. One can also output all types of re/defacing simultaneously.
24 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program has been revamped and updated, including having a new ref vol. Syntax for running this has totally changed (options exist). 24 Jan 2020, P Taylor, @afni_refacer_make_master_addendum, level 3 (MAJOR), type 0 (GENERAL) This program just records additional tweaks to refacer ref vol. Not really meant to be run on its own; for future reference only. 24 Jan 2020, P Taylor, @afni_refacer_make_master, level 1 (MICRO), type 0 (GENERAL) Updated with notes to look at @afni_refacer_make_master_addendum. The addendum program just tweaks the output of this prog.
23 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 4 (ROIs and mask==1 data) Done for J Gonzalez-Castillo.
22 Jan 2020, RW Cox, 3dREMLfit, level 3 (MAJOR), type 6 (ENHANCE) Compute Ljung-Box statistic for -Rvar dataset. Provides a measure of how temporally correlated each voxel's pre-whitened residuals are. Small LB value = good fit by the ARMA(1,1) model. Sub-brick is coded as a chi-squared statistic for use in thresholding in the AFNI GUI. 22 Jan 2020, RC Reynolds, plug_realtime, level 3 (MAJOR), type 0 (GENERAL) add ROIs and data mask method Added corresponding demo: AFNI_data6/realtime.demos/demo_3_ROIs_n_data 22 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 3 (all data light)
21 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Increase thresholds and cbar range in vstat_seedcorr and regr_corr dsets. Clearer QC, methinks, based on several different group dsets.
17 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) New pieces of QC: corr brain image in regr block. Shows corr of mean residual with everything. Have a nice day.
15 Jan 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) corr_* dsets are now correlations with ROI averages They were previously average correlations with each ROI voxel. The new maps look similar, but are probably more natural and have nicer scales. Requested by P Taylor.
14 Jan 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Change text of animal_outs.txt. Add in a couple new dsets to be listed.
13 Jan 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add some make lists ; see 'make list_lists' 13 Jan 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) New pieces of QC: first, seedbased corr maps for non-task data. Second, censor-based warnings (general and per-stim). 13 Jan 2020, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) New function to read in seed list text file. Returns list of seed objs for APQC. 13 Jan 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Couple new options. Can specify colorbar and center coords now.
02 Jan 2020, RC Reynolds, plug_realtime, level 1 (MICRO), type 0 (GENERAL) updates corresponding with Javier's new All_Data_light method
31 Dec 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) Do not require out_limit. Currently will still show in driver. Done for P Taylor.
27 Dec 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 2 (NEW_OPT) New option(s) to not just *check* a dset for FS-ability, but to correct it. The '-fix_all' and accompanying options control this. Bonne idee, DRG!
26 Dec 2019, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT) add -timing_to_1D_mods and -show_events Done for A Gorka. 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. 26 Dec 2019, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Simpler list of uvar dependencies for indiv stim plotting. ... ergo, see indiv stims even if not censoring.
25 Dec 2019, DR Glen, erosion/dilation neighborhoods, level 2 (MINOR), type 5 (MODIFY) Allow for NN1,NN2,NN3 neighborhoods for erosion and dilation 3dAutomask and other programs use these functions the depth option in 3dAutomask gives a depth of automask NN1,2,3
20 Dec 2019, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 6 (ENHANCE) add more help details for advanced usage
17 Dec 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) allow labels as column selectors when reading xmat.1D files Done for G Chen.
12 Dec 2019, RW Cox, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Add -zcensor option Remove from consideration any time point t where xset(t) OR yset(t) is identically zero (in the mask). For Peter Molfese and Emily Finn. Merry X! 12 Dec 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY) More centers - find deepest near voxel closest to Center of Mass Came from CodeConvergence idea by Meghan Robinson Voxel closest to center of mass is similar to latest ICent in Clusterize GUI
10 Dec 2019, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV) Add 'Zoom lock' to the locking capability Also a new environment variable AFNI_ZOOM_LOCK to turn this on at startup, vs interactively later. 10 Dec 2019, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE) add zoom= to SET_WINDOW driver command 10 Dec 2019, RC Reynolds, uber_proc.py, level 2 (MINOR), type 5 (MODIFY) separate into main/lib/gui, so one can run -help w/out PyQt4
09 Dec 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Replace mpeg_encode with ffmpeg in imseq.c From Michael Hanke. He gets the credit and/or blame, as needed. Submitted via github (pull request #39, from 2016). At last! 09 Dec 2019, RC Reynolds, 3dTagalign, level 2 (MINOR), type 2 (NEW_OPT) add -tagset Coded by T Holroyd.
29 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -volreg_opts_ewarp, to pass additional volreg EPI warp options Added for L Fernandino.
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.
26 Nov 2019, RW Cox, @afni_refacer_run, level 3 (MAJOR), type 6 (ENHANCE) Modify shell dataset to avoid some brain clipping Mostly by eroding the inside of the brain shell. Also a couple little tweaks to the script. 26 Nov 2019, RW Cox, 3dQwarp, level 1 (MICRO), type 6 (ENHANCE) Allow user to supply an affine matrix with -resample To re-use a matrix from a previous 3dAllineate run, for speedup 26 Nov 2019, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Add hidden -sincc option for speedup Doesn't seem to help much - faster at large patches but not at smaller patches.
21 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) update babble about FreeSurfer in help 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, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -fs_setup, to optionally source $FREESURFER_HOME/SetUpFreeSurfer.csh 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.
14 Nov 2019, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 0 (GENERAL) New output: fs_ap* dsets for tissue-based reg in afni_proc.py;. New output: *REN_gmrois* dsets for tracking/corr mats in FATCAT. 14 Nov 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-make_rank_dsets ..', bc *rank* dsets no longer make by def. The *REN* dsets should be used instead; opt just for back compatability.
13 Nov 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY) omit any final PyQt4 warnings unless asked for Done to appease the mighty P Taylor. 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
12 Nov 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY) Center for deepest voxel closest to Center of Mass Made in CodeConvergence with Chris Rorden and Meghan Robinson
11 Nov 2019, DR Glen, @suma_acknowledge, level 2 (MINOR), type 1 (NEW_PROG) Make simple graphs of collaborations and classes Made for AFNI bootcamps using SUMA graph datasets This may be useful for acknowledgement for general use
01 Nov 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) process out.mask_at_corr.txt, the anat/template Dice coefficient Requested by P Hamilton. 01 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) create out.mask_at_corr.txt, the anat/template Dice coefficient Requested by P Hamilton.
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.
25 Oct 2019, RW Cox, afni GUI driver, level 2 (MINOR), type 6 (ENHANCE) butpress commands to image viewer butpress=Colr or Swap or Norm to simulate button presses For Paul. 25 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) allow selectors on -dset* options (cannot mix with removal options) Requested by E Finn.
24 Oct 2019, RW Cox, AFNI gui, level 2 (MINOR), type 3 (NEW_ENV) AFNI_IMAGE_COLORSCALE defines colorbar for image viewer window Formerly fixed, now user can specify the color scale to use here from one of these: magma viridis plasma googleturbo Also, I restored the 'g' (gamma) button affect on this color scale. 24 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add combine methods m_tedana, m_tedana_OC Can run tedana from MEICA group: https://github.com/ME-ICA/tedana https://tedana.readthedocs.io
23 Oct 2019, RW Cox, afni GUI, level 1 (MICRO), type 5 (MODIFY) Change dummy dataset creation If NO data is read into afni, then it creates a dummy dataset, since there must be at least one dataset available for the GUI to function. This change makes afni search for some canonical datasets to use in place of the dummy dataset, which will now only be created when one of these datasets is not found. The search is done in the path directory where the afni binary is found (often the user's abin). 23 Oct 2019, RC Reynolds, 3dZeropad, level 1 (MICRO), type 2 (NEW_OPT) add -pad2evens: add needed planes to make each dimension even 23 Oct 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 1 (NEW_PROG) Script to check properties of a dset, see if suitable for FS's recon-all. The check criteria have been built over time, empirically.
22 Oct 2019, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 0 (GENERAL) Adjusted help file. Had given wrong name for opt.
21 Oct 2019, RC Reynolds, afni, level 1 (MICRO), type 2 (NEW_OPT) add -get_running_env, to show env including locally set vars 21 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Display AFNI environment vars in the terminal, via new opt: -env. Makes good bedtime reading. 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. 17 Oct 2019, RC Reynolds, 3dANOVA, level 1 (MICRO), type 6 (ENHANCE) improve descriptions of some option errors to the user 17 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Display AFNI Tips in the terminal, via new opt: -show_tips. Will be used+parsed for the HTML RST docs.
16 Oct 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 6 (ENHANCE) re-insert updates from 2019.05.29, plus updates for -init_xform 16 Oct 2019, RC Reynolds, TwotoComplex, level 1 (MICRO), type 6 (ENHANCE) process entire time series, rather than just first volume(s) Done to further the quest of A Khojandi for world domination. 16 Oct 2019, RC Reynolds, 3dFFT, level 1 (MICRO), type 6 (ENHANCE) process entire time series, rather than just the first volume Done for A Khojandi.
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. 15 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -subbrick_info, to write only 'At sub-brick #N' info to stdout
11 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) checked and merged another 17 commit PR from pn2200 This is mostly to resolve missing prototypes.
10 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -niml_hdr, to write full NIML header(s) to stdout 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
09 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) checked and merged 30 commit PR from pn2200 This is mostly to resolve compiler warnings.
07 Oct 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) probably the last set of test updates for now 07 Oct 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Change text of animal_outs.txt. Minor 'under the hood' changes, too. 07 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Simpler opts for package and version number. For scriptability.
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.
03 Oct 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 0 (GENERAL) Just divvied up the behavior of the functions better. Also have a general, NxN case . 03 Oct 2019, P Taylor, epi_b0_correct.py, level 1 (MICRO), type 0 (GENERAL) Calculate oblique transform differently; use 3dWarp instead of cat_matvec. Probably negligible practical change. 03 Oct 2019, P Taylor, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) Fancy new function to calculate if a list-matrix is square. ps: not that fancy.
02 Oct 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) The naming convention of PE dist dir has been reversed; mask opts changed. PE dist dir should match with JSONs better; 3dmask_tool does masking now. 02 Oct 2019, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 0 (GENERAL) Output more specific information about finding unexpected negative values. Tell user the [row, col] of potentially bad values, for easier QC.
30 Sep 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) added test scripts under commands, along with cmake versions for build
26 Sep 2019, RC Reynolds, NIFTI, level 1 (MICRO), type 5 (MODIFY) nifti_read_ascii_image no longer closes fp or free's fname
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.
18 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) if -html_review_style pythonic, check for matplotlib
16 Sep 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) check on /usr/local/bin/python* files, as is done with /sw/bin
13 Sep 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) report XQuartz version As suggested by P Taylor. 13 Sep 2019, P Taylor, 3dWarp, level 2 (MINOR), type 2 (NEW_OPT) New opt: -disp_obl_xform_only. Better way to get transform between obl coords than cat_matvec trickery.
12 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) add file tracking and -show_tracked_files option In preparation for shifting evil for P Taylor and D Glen. 12 Sep 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) Output QC directory of images now, as well. Useful for quick QC. Later, will add some checks for obl, to not smooth unnec. 12 Sep 2019, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Use 'mkdir -p' with odir now. Simplifies scripts using it.
10 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Unifize output in standard space. Better for visualization in afni_proc.py QC. 10 Sep 2019, P Taylor, epi_b0_correct.py, level 1 (MICRO), type 0 (GENERAL) Fix help descriptions (thanks L. Dowdle for fixes). Also add '-hview' capability.
09 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) add control for 3dDespike -NEW25 Requested by aparekh on the Message Board.
06 Sep 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Two minor changes: montages now separated by 1 gap line. ... and show censor bars in VR6 plots, if censoring. 06 Sep 2019, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Now use montgap=1 by default. This is for APQC applications, where subj data fills FOV. 06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Output skullstripped version of template in std space. Also add 'notes' to that file, so gen_ss*script* can find template. 06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Put QC images into subdir called QC; output mask. Few other tiny changes/reorganizations internally.
05 Sep 2019, RC Reynolds, SurfMeasures, level 1 (MICRO), type 5 (MODIFY) retab and fix indentations
04 Sep 2019, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 6 (ENHANCE) check for valid 'mris_convert --help' output 04 Sep 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opts: -obl_resam_ulay OIU, -obl_resam_Olay OIO, -obl_resam_box OIB. Control resampling of dsets (ulay, olay, focus box) when applying obl. 04 Sep 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-extra_fs_dsets ..', to translate more FS-created surf/ dsets. Allow more FS surf dsets to be brought into SUMA. For F. Lalonde.
03 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New QC imaging with @chauffeur_afni; mask created, too. And a few minor changes under the hood, worked out with DRG.

auto-generated by afni_history on Sep 1 2021