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_months 6 

---- 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).

auto-generated by afni_history on Sep 1 2021