AFNI HISTORY

all levels

The levels of importance go from 1 to 5, with meanings:
       1 - users would not care
       2 - of little importance, though some users might care
       3 - fairly important
       4 - a big change or new program
       5 - IMPORTANT: we expect users to know


generated via the command : afni_history -html -reverse -type BUG_FIX 

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

auto-generated by afni_history on Oct 17 2019