AFNI HISTORY

level 2 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 2 -past_years 1 

---- 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.
20 Aug 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -write_tsv_cols_of_interest
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
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.
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.
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, 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, 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.
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, 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.
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).
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.
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.
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.
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
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.
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.
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.
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
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.
16 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) simplify logic in THD_mask_erode(), with negligible slowdown
15 Mar 2021, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT) add convenience options -perclist and -perc_quiet
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.
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.
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
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.
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.
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, 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, 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.
29 Dec 2020, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with nifti_clib
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.
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.
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.
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?)
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.

auto-generated by afni_history on Sep 1 2021