AFNI HISTORY

level 1 and higher

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


generated via the command : afni_history -html -reverse -min_level 1 -past_years 2 

---- log of AFNI updates (most recent first) ---- 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. 09 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -write_3dD_script and -write_3dD_prefix
08 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added options -rank, -rank_style, -reverse_rank
07 May 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Add -Qfinal option (experimental) 07 May 2013, DR Glen, 3dAnatNudge, level 2 (MINOR), type 5 (MODIFY) always produce output with -prefix even if no shift
06 May 2013, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT) Add -short option == save results as shorts For use in warping label datasets. 06 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) added -regress_anaticor example; opt implies -mask_segment_anat/_erode 06 May 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) added option -slice_timing 06 May 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added option -transpose_write
03 May 2013, RW Cox, thd_compress.c, level 1 (MICRO), type 5 (MODIFY) Substitute pigz for gzip and pbzip2 for bzip2 if present in path 03 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -regress_anaticor and -mask_segment_erode Use the -regress_anaticor option to regress the WMeLocal time series. This is the ANATICOR method of HJ Jo.
01 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY) Minor updates Make -emask work with -duplo. Add SAMPLE USAGE section to help to show how to combine 3dAllineate with 3dQwarp, and/or align_epi_anat.py also. Add -base and -source options, to make program look more like 3dAllineate. 01 May 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 6 (ENHANCE) added -help example for -show_trs_uncensored
29 Apr 2013, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE) set AFNI_NO_OBLIQUE_WARNING in scripts
26 Apr 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY) Make -emask option work correctly with -duplo 26 Apr 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_trs_censored/_uncensored (mostly for X-matrix datasets)
25 Apr 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) strlist chooser stays in same place if re-opened - for Allison
24 Apr 2013, RC Reynolds, @move.to.series.dirs, level 2 (MINOR), type 1 (NEW_PROG) partition a list of DICOM files by series number Done for I Shapira. 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. 24 Apr 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -censor_next_TR Sticking with backward diff for deriv, as it makes sense for censoring.
23 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) added eroded ROIs for -regress_ROI: WMe, GMe, CSFe
22 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Added -out1D option to output correlations in text format. 22 Apr 2013, RW Cox, 3dNwarpAdjust, level 2 (MINOR), type 1 (NEW_PROG) For template-building via @toMNI_Qwarp Computes the mean warp, and adjusts the individual warps to get rid of this mean warp (under the presumption that it is some kind of bias). 22 Apr 2013, RC Reynolds, auto_warp.py, level 2 (MINOR), type 0 (GENERAL) modified afni_base.afni_name.new() with 2 cases of parse_pref=1 This is currently the only application of that parameter.
19 Apr 2013, DR Glen, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT) lpi xyz output option
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. 16 Apr 2013, RC Reynolds, 3dmaskave, level 2 (MINOR), type 2 (NEW_OPT) added -sumsq (sum squares) and -enorm (Euclidean norm) options
15 Apr 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) added RESTING STATE NOTE to help 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.
12 Apr 2013, RW Cox, 3dLocalHistog, level 2 (MINOR), type 1 (NEW_PROG) Collecting counts of labels in nbhd of each voxel For building atlases that allow for uncertainty in position 12 Apr 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) detach from terminal and graph fading are now the defaults
09 Apr 2013, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added options for providing orts for each input time series See options -*_orts in the help output. 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.
05 Apr 2013, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE) added Help web link to class handouts 05 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) revert -save_orig_skullstrip to -save_skullstrip This should have no effect on results, except for rename of anat_strip to anat_ns. It also gets around a temporary name change from AEA.py.
04 Apr 2013, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -Apair option For testing differences in correlations in 1 group from 2 different seeds -- the regular seed minus the 'Apair' seed. Also changes to AFNI to set the Apair seed, etc.
02 Apr 2013, RW Cox, Nwarp, level 1 (MICRO), type 0 (GENERAL) Replace sqrt(nwarp) algorithm Schulz method gives unpleasant ringing artifacts in the square root. Use the Denman-Beavers methods instead, which is slower and maybe a little less accurate, but doesn't do the ringing weirdness.
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, ZS Saad, 3dAutoTcorrelate, level 1 (MICRO), type 2 (NEW_OPT) Added option -mask_source 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.
29 Mar 2013, DR Glen, general compression, level 2 (MINOR), type 3 (NEW_ENV) pigz for faster gzip-like compressionpigz is a gzip utility that makes use of multiple CPU's. It produces and uses .gz files. To use, set AFNI_COMPRESSOR to PIGZ.
28 Mar 2013, ZS Saad, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX) Parsing of -on* and -off* options failed for non-integral values
27 Mar 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_group_labels, -label_prefix_keep/_drop Option -label_prefix_drop can be used to remove bandpass regs for 3dRSFC. 27 Mar 2013, DR Glen, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT) absolute value of voxels for statistics
26 Mar 2013, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added option -inflate for automatic creation of semi-inflated surfaces See @SUMA_Make_Spec_FS -help for details 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 26 Mar 2013, ZS Saad, suma, level 1 (MICRO), type 5 (MODIFY) AlignToExperiment transforms no longer applied to spherical surfaces This makes spheres show up better by default in SUMA for prying. 26 Mar 2013, ZS Saad, SurfSmooth, level 1 (MICRO), type 2 (NEW_OPT) Added -match_center to force recentering of smoothed surfaces. SurfSmooth -help for details 26 Mar 2013, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) Add option -cmeth (MEAN or MEDIAN) for Steve Gotts 26 Mar 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Minor changes to Fade feature in graph viewer Toggle button in Opt menu. AFNI_GRAPH_FADE environment variable. Make sure it works with Clusterize and InstaCorr updates.
25 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Merged handling of CoordBias with Prying, all in VisX Lots of annoying little details there. See functions like: SUMA_*CoordBias*, SUMA_ApplyVisXform(), and SUMA_Apply_VisX_Chain() 25 Mar 2013, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT) More voxelwise neighborhood shapes available. Voxelwise neighborhoods can be any sphere/radius size, and even ellipsoidal. Some memory stuff should be better as well.
22 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added stippling for line segments DOs, see SUMA's ctrl+h for details. 22 Mar 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Fading of graph sub-windows with the 'F' key
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, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) NearestNodeCoords was added to -output_params 14 Mar 2013, ZS Saad, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) -init_xform now takes AUTO_CENTER_CM and CENTER_CM 14 Mar 2013, P Taylor, 3dNetCorr, level 4 (SUPER), type 1 (NEW_PROG) New function: calculate correlat/Z of ROIs in a network. This program works on several networks as separate subbricks simultan- eously. 14 Mar 2013, P Taylor, rsfc, level 2 (MINOR), type 5 (MODIFY) New functions; streamline some other functions. For addition of 3dNetCorr, mainly. 14 Mar 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 5 (MODIFY) List ROI labels near start of *.grid; use floor to get NmNsThr This allows for more similarity with 3dNetCorr, and might be useful as well if the labeling of ROIs in a network is not just 1,..,max. The flooring vs ceiling is so that people don't have to use 0.00099 as a relative fraction of MC iterations to get the number they want. 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.
12 Mar 2013, RW Cox, 3dNwarpApply, level 2 (MINOR), type 2 (NEW_OPT) Various fixes -ainterp = lets you interpolate data differently from warp -affter = lets you use a different affine warp for each sub-brick -nwarp = allow catenation and inversion directly on the command line These last 2 options make the program 3dNwarpCat pleonastically redundant. 12 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) Handling input and output directories Output now goes to current directory (./) unless otherwise specified with -output_dir. Thanks a lot, Rick.
11 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) Handling input and output directories Output follows input directories unless specified with -output_dir Previously, all input files had to exist in current directory. Changes allow for output to follow anat or epi dataset directories or specified output directory. Also minor change to call tcsh without sourcing startup .cshrc 11 Mar 2013, DR Glen, @Atlasize center of mass, level 2 (MINOR), type 2 (NEW_OPT) Add -centers for center of mass locations in atlas regions -centers option added to @Atlasize and @MakeLabelTable This location is simple center of mass for now and may be outside region for non-blobbish regions
08 Mar 2013, RC Reynolds, 3dTcat, level 2 (MINOR), type 2 (NEW_OPT) added -TR and -tpattern options
07 Mar 2013, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE) handle -prefix and -overwrite for -show_bad_backslash The combination can be used to 'fix' bad files.
27 Feb 2013, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT) Added -GM option to stretch gray matter to a consistent-ish place 27 Feb 2013, RC Reynolds, python-general, level 1 (MICRO), type 2 (NEW_OPT) added Ziad's apsearch global options: -all_opts, -h_find, -h_view
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Prying hemispheres apart to see medial or lateral sides simultaneously This is controlled via the ctrl+Button 1-Motion. See SUMA's ctrl+h output for details. The prying behaviour is different for spheres and flat maps Just try it and see. ctrl+double click to get back to initial view. See also env: SUMA_LHunify 22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Automatically adjust position of LR surfaces so that they don't overlap This is only done for anatomically incorrect surfaces, the others should not overlap of course. This allows for simultaneous viewing of inflated surfaces and flattened ones side by side. 22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Option -anatomical labels all -i_* -t_* surfs anatomically correct 22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Option -onestate put all -i_* surfs on command line in the same state 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, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV) SUMA_LHunify to automatically merge LR hemispheres in all views This is done by discarding the _lh _rh to state names that are created by @SUMA_Make_Spec_FS 22 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT) Instead of just individual ROI masks, can get map of Ntracks/voxel. This allows a posteriori thresholding/comparisons/analysis. 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.
21 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) small help update to include tshift block in example 5c Thanks to J Gonzalez bringing it up.
20 Feb 2013, RW Cox, 3dUnifize, level 2 (MINOR), type 1 (NEW_PROG) Quick and dirty approximate spatial uniformization of T1 anats Mostly for use with 3dQwarp
19 Feb 2013, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV) Histogram plugins can now do cumulative distributions set AFNI_HISTOG_CUMULATIVE to YES
15 Feb 2013, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Added -FNameNoAfniExt to -out option 15 Feb 2013, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Allowed script to work with NIFTI input for both -surf_anat and -exp_anat
14 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Added stippling-based transparency to surface viewing. Fancier blending-based transparency will have to wait. 14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 2 (NEW_OPT) Option -nocor to improve data import from FreeSurfer Option avoid COR images, produces NIFTI and GIFTI output that aligns with the initial volume passed to FreeSurfer. This required considerable changes to the script and will not be the default for a while longer. 14 Feb 2013, ZS Saad, apsearch, level 2 (MINOR), type 5 (MODIFY) Improved parsing for options to avoid getting options from sample commands Previously, if you used an example in the help that called a different program and you used options on clean lines as part of that example command, those options would get attributed to the program whose help you're reading. Pfew. Not anymore. 14 Feb 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -TransMode to control surface transparency. 14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 1 (MICRO), type 2 (NEW_OPT) Option -set_space set space of output volumes 14 Feb 2013, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT) Add -emask option (exclude certain voxels) For use in registering pre- and post-surgery volumes (e.g.). 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.
13 Feb 2013, RC Reynolds, unix_tutorial, level 3 (MAJOR), type 1 (NEW_PROG) added tutorial to CVS tree, with processed files under AFNI_data6 13 Feb 2013, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE) inform user of subj_dir when writing AP command
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
11 Feb 2013, RC Reynolds, file_tool, level 1 (MICRO), type 6 (ENHANCE) help updates
07 Feb 2013, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Add MASK= to driver for INSTACORR INIT Per the request of the esteemed Daniel Handwerker, scientist extraordinaire. 07 Feb 2013, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Added Greg Baxter's (UCSD) change for b-matrix input
06 Feb 2013, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Merged Paul Taylor's recent code changes Also created afni_history_ptaylor.c see afni_history -author ptaylor for details on the changes 06 Feb 2013, ZS Saad, MakeColorMap, level 2 (MINOR), type 2 (NEW_OPT) -suma_cmap, -usercolutfile, and -sdset* options for SUMA colormaps The new options allow users to create SUMA's colormaps with labels and turn datasets into labeled datasets with the user's colormap 06 Feb 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) -labelize for assigning a SUMA colormap to an integral valued dset 06 Feb 2013, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added special filename '1D:stdin' to make mri_read get 1D from stdin In this manner, most 3d programs can now accept stdin input in 1D format This change was suggested by Isaac Schwabacher. 06 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT) Add ability to output each WM-region mask as an individual ROI. This should make it simpler to use an ROI as a mask than with the 2^(ROI number) labelling system within subbrick outputs. 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. 05 Feb 2013, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) updates to the help introduction
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
01 Feb 2013, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV) SUMA_ContourThickness to control the tickness of dset contour lines Addition made in response to Valentinos' feedback. Documentation is in .sumarc file.
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.
30 Jan 2013, RC Reynolds, python-general, level 2 (MINOR), type 6 (ENHANCE) added less biased correlations and various gcor utility functions
24 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE) be able to process a run of AFNI volumes (-file_type AFNI) added for Der-Yow Chen and Cecil Yen 24 Jan 2013, RC Reynolds, 3dinfo, level 1 (MICRO), type 5 (MODIFY) get -orient output via new THD_fill_orient_str_3
22 Jan 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Added -bash option for bash filename completion, & -recreate_all_afni_help Thanks be to Isaac Schwabacher. 22 Jan 2013, ZS Saad, HalloSuma, level 2 (MINOR), type 1 (NEW_PROG) A sample light-weight program to illustrate 2-way communication with AFNI The program can be compiled in C or C++ along with the NIML library without having to link to AFNI/SUMA libraries. Documentation is the code. 22 Jan 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -echo_nel(*) option to show NIML communication elements 22 Jan 2013, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Added -hand for handeness of orientation 22 Jan 2013, ZS Saad, 3dLocalstat, level 1 (MICRO), type 5 (MODIFY) THD_localstat() was not applying mask to output under resam. mode 22 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -file_type, in prep for reading AFNI/NIfTI images
18 Jan 2013, RC Reynolds, @compute_gcor, level 2 (MINOR), type 1 (NEW_PROG) compute GCOR = global correlation of a dataset 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.
16 Jan 2013, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT) added option -dc_params To go with new scripts AFNI_data6/realtime.demos/demo.2.fback.*. 16 Jan 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added option -show_gcor (and _all and _doc) compute GCOR (average correlation) on 1D files
11 Jan 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -flip_orient option to change orientation of triangles.
09 Jan 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added option -regress_compute_gcor If errts and EPI mask exist, GCOR is computed by default.
07 Jan 2013, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT) Added -radial_* options to test SUMA_Volume_RadFill() function. 07 Jan 2013, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) added option -l2norm, to compute L2 norm
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, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY) Allow use of Spearman rather than Pearson for scatterplot correlation Set via environment variable AFNI_CLUSTER_SPEARMAN, or by popup menu attached to top of clusterize report form. This is for PK. 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() 27 Dec 2012, RW Cox, 3dPolyfit, level 1 (MICRO), type 2 (NEW_OPT) Add '-base' option To allow fitting (in space) arbitrary input images, as well as (spatial) polynomials.
26 Dec 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) -virtvec option for Javier
21 Dec 2012, ZS Saad, @clip_volume, level 1 (MICRO), type 2 (NEW_OPT) Added options -crop_allzero and -crop_greedy. 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.
19 Dec 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL) Update from Rayus for handling .nii files.
18 Dec 2012, ZS Saad, cat_matvec, level 1 (MICRO), type 2 (NEW_OPT) option -4x4 to output augmented matrix. 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.
05 Dec 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY) add Detrend button to Opt menu Detrends each time series before plotting. For Javier. 05 Dec 2012, RC Reynolds, serial_helper, level 1 (MICRO), type 0 (GENERAL) added useless string specifier in snprintf to block compier warnings Requested by Y Halchenko.
03 Dec 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY) Added temporary overwriting without upsetting initial setting See THD_get_ok_overwrite() 03 Dec 2012, ZS Saad, 3dSkullStrip, level 1 (MICRO), type 5 (MODIFY) More modifications for head extraction Approach now uses 'Radial Stats' for head/non-head separation. See functions SUMA_THD_Radial_HeadBoundary(), SUMA_ShrinkSkullHull_RS() and SUMA_ExtractHead_RS()
29 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) add -f to 'tcsh -c' for getting output from commands Thanks to P Molfese for the suggestion to avoid .cshrc text output.
28 Nov 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) -dospcov Compute Spearman correlation of subject results with covariate. Output sub-bricks are labeled with '_SP' at the end, as in 'LLL_cov_SP' to indicate the group with label 'LLL' correlated with the covariate with label 'cov'. This is for the IMom (PK).
26 Nov 2012, RC Reynolds, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) added -save_script option added script history in afni_com class
23 Nov 2012, RW Cox, afni instacorr, level 2 (MINOR), type 5 (MODIFY) Allow Start and End indexes, rather than Ignore (=Start) To allow Instacorr-ing a subset of a time series. Per the request of the Exceptional Javier Gonzalez-Castillo
15 Nov 2012, ZS Saad, AFNIio.R, level 2 (MINOR), type 5 (MODIFY) Made read.AFNI and write.AFNI more clever Changes included: AUTO method selection, dset.attr() improvements to handle dset structures or their headers from either clib or Rlib functions. Micro change to THD_dblkatr_from_niml which crashed for null strings. 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. 15 Nov 2012, RC Reynolds, 3dTqual, level 2 (MINOR), type 2 (NEW_OPT) added -mask option Requested by evangelou.
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.
12 Nov 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT) Straight and weighted divisions of T1 by PD, and initial alignment The weighted volume allows one to keep the high-res. aspect of PD division, while considerably reducing the extreme enhancement. 12 Nov 2012, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT) Added -cmask and -quiet to 3dHist
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.
06 Nov 2012, ZS Saad, 3dkmeans, level 2 (MINOR), type 2 (NEW_OPT) Added -write_dists to only output ascii files when users want them The changes were made to also cleanup the output of 3dSeg. 06 Nov 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 2 (NEW_OPT) Added -head*, and -cut_below options to generate whole head masks This was needed because 3dAutomask or 3dSkullStrip would fail atcreating w hole head masks for cases with coil-array shading problems and/or lots of noise.
01 Nov 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV) Abide by AFNI's AFNI_FLOATSCAN variable and look for bad values SUMA will now scan for bad floats (NAN, and INF) and sets them to 0, when the dataset is loaded. You can turn this feature off with AFNI_FLOATSCAN set to NO. 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.
19 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE) added test for BOM bytes (byte order mark) 19 Oct 2012, G Chen, 3dMVM, level 3 (MAJOR), type 1 (NEW_PROG) Multivariate modeling approach to group analysis This is an R program that performs conventional ANOVA or ANCOVA-type analysis with no limit on the number of variables. See more details at http://afni.nimh.nih.gov/sscc/gangc/MVM.html
18 Oct 2012, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV) AFNI_CREEPTO modifies 'jumpto xyz' behavior 18 Oct 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 4 (BUG_FIX) small updates to correspond with library changes 18 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE) added convenience option -test
17 Oct 2012, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL) Add 'j' and 'f' keystrokes for image viewers Like 'Jump' and 'Flash' in the Clusterize Rpt windows, for the cluster in which the crosshairs currently reside. 17 Oct 2012, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT) added -no_length option, which helps when running diffs on output 17 Oct 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) removed unneeded -set_tr from 1d_tool.py -censor_motion
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, ZS Saad, 3dSurfMask, level 1 (MICRO), type 2 (NEW_OPT) Option -no_dist to avoid length distance computations. Also, the fast method was improved per the comment below. 16 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added analysis type and processing block list 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, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT) A better masking option using -brainhull The option seems pretty good at creating brain mask from pretty lousy data. 15 Oct 2012, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Add 'range=a,b' option to ALTER_WINDOW command in AFNI driver 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.
13 Oct 2012, ZS Saad, 3dHist, level 2 (MINOR), type 1 (NEW_PROG) Computes histograms using functions from the segmentation routines The program uses heuristics to automatically select histogram parameters, and it allows histogram queries. It had to be separate from 3dhistog because it uses libSUMA.a and because the latter's interface was getting too complicated. 13 Oct 2012, ZS Saad, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) -voxvol returns a voxel's volume in mm cubed
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, afni-general, level 2 (MINOR), type 6 (ENHANCE) added byte-swapping for complex numbers in thd_niml.c 12 Oct 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) included tshift block in example #9 - resting state analysis Thanks to D Drake for reminding me to add it. 12 Oct 2012, RC Reynolds, @RetinoProc, level 1 (MICRO), type 4 (BUG_FIX) set AEA_opt in quotes, as it might be a list
10 Oct 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added yoking of 1_only, Dim, and Opacity controls 10 Oct 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -Opa to control opacity 10 Oct 2012, ZS Saad, @RetinoProc, level 1 (MICRO), type 2 (NEW_OPT) Option -AEA_opts for passing arguments to align_epi_anat.py
09 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allow input of surface-based complex time series. SUMA will report and graph the magnitude of complex data Other transformations can be added when needed. Surface data I/O were modified to allow handling of complex-typed data including functions in thd_niml.c, and thd_gifti.c Programs like 3dDFT and 3dcalc can read/write complex surface- based datasets. 09 Oct 2012, ZS Saad, 3dDFT, level 2 (MINOR), type 2 (NEW_OPT) Allow handling of complex surface-based data Earlier versions could not output complex data for surface-based datasets. Minor changes to the help output to fix order of -cx2r option and allow option suggesting. 09 Oct 2012, ZS Saad, 3dttest++, level 1 (MICRO), type 5 (MODIFY) Micro modification of verbose output to flag paired from unpaired tests 09 Oct 2012, ZS Saad, 3dcalc, level 1 (MICRO), type 5 (MODIFY) Clarify help for -cx2r, and allowing -help in mid command.
05 Oct 2012, RC Reynolds, dicom_hinfo, level 2 (MINOR), type 2 (NEW_OPT) added option -no_name 05 Oct 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added option -quick_censor_count
04 Oct 2012, ZS Saad, afni-matlab, level 2 (MINOR), type 2 (NEW_OPT) Minor tweaks to WriteBrik and BrikInfo WriteBrik can automatically set some header fields (AdjustHeader option) BrikInfo now loads IJK_TO_DICOM_REAL 04 Oct 2012, ZS Saad, MapIcosahedron, level 1 (MICRO), type 4 (BUG_FIX) Dset Mapping failed on sparse datasets, at times. 04 Oct 2012, ZS Saad, 3dedge3, level 1 (MICRO), type 5 (MODIFY) Updated 3DEdge library to GPL version: 2012-02-22
03 Oct 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) dashed parameters are now illegal for many options in many python programs Affects programs: 1d_tool.py, afni_proc.py, gen_group_command.py, make_random_timing.py, make_stim_times.py, option_list.py, timing_tool.py
02 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE) added stim_type column to stim table This corresponds to the afni_proc.py option -regress_stim_types. 02 Oct 2012, RC Reynolds, model_conv_diffgamma, level 1 (MICRO), type 0 (GENERAL) small help update
01 Oct 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) added 'file' to list of -stim_types parameters The 'file' type would imply -stim_file in 3dDeconvolve, not timing.
28 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's map_TrackID to warp tracks by an affine transform 28 Sep 2012, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) Enabled automatic centering via -init_xform You can use -init_xform AUTO_CENTER or -init_xform CENTER to perform center alignment during registration. 28 Sep 2012, ZS Saad, @T1scale, level 2 (MINOR), type 1 (NEW_PROG) A mini script to scale T1s by PD volumes Script uses method borrowed from @CalculateSignatures to reduce bias field in T1 using a PD volume. Script also works well without PD. 28 Sep 2012, ZS Saad, 3dTrackID, level 1 (MICRO), type 2 (NEW_OPT) Option -rec_orig to record dataset origin in tractography output
26 Sep 2012, RC Reynolds, nifti_tool, level 2 (MINOR), type 4 (BUG_FIX) changed ana originator field from char to short 26 Sep 2012, RC Reynolds, @update_afni_binaries, level 2 (MINOR), type 2 (NEW_OPT) added -apsearch; verify download for recursive step
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, @SUMA_Make_Spec_Caret, level 1 (MICRO), type 5 (MODIFY) Updated script to work with current Caret release 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
21 Sep 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY) pkundu update 21 Sep 2012, RC Reynolds, 3dNLfim, level 1 (MICRO), type 0 (GENERAL) added ConvDiffGam to help
20 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) added some projection function to python libraries 20 Sep 2012, RC Reynolds, 3dClustSim, level 1 (MICRO), type 0 (GENERAL) added a note to the help about computing blur estimates Requested by J Weisberg.
19 Sep 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -scale option for the Person from Kolkata
18 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Checked in Prantik Kundu's MEICA tools. Try meica.py -help, also try @Install_MEICA_Demo
13 Sep 2012, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT) Added -pdf to 3dhistog to make area = 1 13 Sep 2012, RC Reynolds, afni_util, level 2 (MINOR), type 6 (ENHANCE) can call list functions via -listfunc (to avoid input formatting) Also, use -join after the LISTFUNC to remove list format on output, e.g. cd AFNI_data6 afni_util.py -listfunc list_minus_glob_form -join group_results/OLSQ*.HEAD 13 Sep 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) download and run the current version on the web site Good idea, Bob.
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 5 (MODIFY) Began merger of surface controllers The idea is to have all surface controllers in one window in order to save on screen space. Looks promising but must be rolled out carefully because surface controllers permeate everything.Use e nvironment variable SUMA_SameSurfCont to turn feature on. Make sure it is debugged with valgrind too. 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()
07 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) SUMA now highlights cluster |max|, rather than max
06 Sep 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added -no_volreg for time series already registered 06 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX) SUMA's sub-brick arrowfields were not updating properly 06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) if varying facs/types on NIfTI write, write floats instead of failing 06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) apply global opt -pad_to_node when going through AFNI format in thd_niml.c 06 Sep 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY) print missing xmat error w/out debug, as it is fatal
05 Sep 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT) Added possiblity to scale by top percentiles with -FATscl This would produce .sc9 outputs. It looks like the scaling is more promising than by MEDIAN(20) or MAD(20). 05 Sep 2012, ZS Saad, 1dRplot, level 2 (MINOR), type 2 (NEW_OPT) Made program take in histograms produced by 3dGenFeatureDist This required changes to AFNIio.R so that NIML groups are not automatically sent to the distbin. Instead, the first element in the ni_group is returned. 05 Sep 2012, ZS Saad, 3dGenFeatureDist, level 1 (MICRO), type 2 (NEW_OPT) Program now creates the feature correlation matrix per class. Both histograms and correlation matrices are stored in NIML format under a directory named by the user.
04 Sep 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) Made program output niml 1D format, makes it easy to plot with 1dRplot 04 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added option -regress_ROI This allows for tissue-based regression, with ROI averages from any of: brain (from full_mask), GM, WM and CSF (from Classes_resam) The 'mask' block is required for all ROIs, and option -mask_segment_anat is required for the latter 3. 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.
31 Aug 2012, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) added option -signed_absmax Requested by P Hamilton.
30 Aug 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) Made program create corr. matrix as opposed to just one pair of sub-bricks Output is also beautified with option -show_labels 30 Aug 2012, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 5 (MODIFY) display -show_mmms output to 4 places
29 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Allowing yoking of intensity to node selection. Ctrl+Button-3 would select a node and switch intensity sub-brick to that node's index * K. This is only done if the dataset currently viewed has as K times as many sub-bricks as the surface has nodes. K being an integer, naturally. Nick Oosterhoff instigated this business 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 2 (NEW_OPT) Preserved controller settings for newly loaded or reloaded dsets The preserved settings include clustering options. 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.
27 Aug 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY) Modifed THD_load_tcat() to include subbrick labels in auto catenation Also, started checking for datatype mixing and issuing warning when needed .
24 Aug 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Added interactive clustering to surface controller The state of affairs: -Clustering tables are only output to the terminal and the log window. -Clustering is yoked between hemispheres -Can control connectivity radius and min area or min nodes -When you click on a node inside a cluster, the node in that cluster with the highest value is highlighted with a black sphere. 24 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's 3dRSFC to the distribution 24 Aug 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT) Added coordinate feature generation, if TLRC xform is provided Note that the TLRC xform need not be too precise. The coordinate features are not intended to make sure of segmentation templates. 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, niprobe, level 1 (MICRO), type 1 (NEW_PROG) A variant on niccc to handle certain NIML file probing operations 24 Aug 2012, ZS Saad, SurfClust, level 1 (MICRO), type 2 (NEW_OPT) Allow -i* form of surface input 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. 24 Aug 2012, ZS Saad, @SUMA_Make_Spec_FS, level 1 (MICRO), type 5 (MODIFY) Made script port more datasets from FreeSurfer (depth, curvature) 24 Aug 2012, RC Reynolds, column_cat, level 3 (MAJOR), type 1 (NEW_PROG) like 'cat', except horizontally (see recent Unix command, 'paste')
23 Aug 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT) can pass -censor_dset
21 Aug 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 2 (NEW_OPT) added 'sigma' uvar, for passing to SurfSmooth
20 Aug 2012, ZS Saad, SurfExtrema, level 1 (MICRO), type 2 (NEW_OPT) Made default input the convexity of the surface
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
16 Aug 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 5 (MODIFY) show datasets names when a 'labels not unique' error occurs
15 Aug 2012, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) Added -sublabel_prefix and -sublabel_suffix 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, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) match default class order for 3dSeg; copy labeltable into resampled dset 14 Aug 2012, DR Glen, whereami minimum probability, level 2 (MINOR), type 2 (NEW_OPT) Minimum probability option to consider for probabilistic atlases Can set option, -min_prob, or environment variable, AFNI_WHEREAMI_PROB_MIN, to control output of whereami reports or masks from probabilistic atlases 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
10 Aug 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL) Updates from Rayus. Fixed bugs with -outcensor and -snr. Added -bpassregs and -keepuncensored. Use variable detrending for -tsnr.
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, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY) Improved handling of coords in 'cm' units and better axis text layout Surfaces with coords in cm were poorly displayed and without warning. Now you are urged to make use of the SUMA_NodeCoordsUnits env . Axis text labels were also improved to reduce clobbering. 08 Aug 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -use_slice_loc; fixed app of use_last_elem in mri_read_dicom g_info.use_last_elem has usurped the lone global 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
06 Aug 2012, DR Glen, NIFTI reading, level 2 (MINOR), type 3 (NEW_ENV) Handling view equivalents for NIFTI AFNI_NIFTI_VIEW sets default view for AFNI datasets marked as 'aligned' (sform_code or qform_code = 2). This variable should be set to 'TLRC', 'ORIG' or 'ACPC'.
03 Aug 2012, RW Cox, 2perm, level 1 (MICRO), type 1 (NEW_PROG) For generating 2 random subsets of a sequence of integers
31 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) have -mask_segment_anat default to no (libgsl is not quite so common) 31 Jul 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) speed up reading NIfTI files with long histories (THD_dblkatr_from_niml) Thanks to J Gonzalez for reporting the problem. 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.
30 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) if surface analysis, create run_suma script 30 Jul 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_mmms Display min, mean, max, stdev of each column.
26 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL) Modify wsinc5 (again) to be more flexible 26 Jul 2012, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_comm_times option to show communication times Added for J Evans (and to get it off an ancient todo list). 26 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -mask_segment_anat and -mask_rm_segsy If anat is stripped, create segmented anat unless user says not to. 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.
23 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL) Also, change wsinc5 taper from Hanning to Hamming 23 Jul 2012, RW Cox, 3dAllineate, level 1 (MICRO), type 3 (NEW_ENV) Allow 7x7x7 interpolation in wsinc5 + spherical mask via environment variables 23 Jul 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) allow programs to read auto-tcat datasets using filelist:DSETS.txt If DSETS.txt contains a list of datasets, they will be read in using THD_open_tcat(), as if they were listed separated by spaces. Added for C Connolly.
20 Jul 2012, RC Reynolds, apsearch, level 1 (MICRO), type 5 (MODIFY) exclude README.* from program list Executable README files can be troublesome...
19 Jul 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Allow for L/R hemi yoking for many operations These include:Threshold setting. I,T,B sub-brick selection. Range setting. Dset loading. Cmap changing. Dset switching. Order changing. 19 Jul 2012, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV) New variables to initialize range setting and symmetric range See SUMA_Auto_I_Range, SUMA_Auto_B_Range, and SUMA_Sym_I_Range in ~/.sumarc . If you don't see them, time to run: suma -update_env
18 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG) Added Paul Taylor's 3dReHo to the distribution
17 Jul 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) added checks for volreg and uncensored X-mat; get view from volreg 17 Jul 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 5 (MODIFY) removed -Niter opt from SurfSmooth (let it decide)
12 Jul 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) added ':a:b:c' appendage to -stim_times_AM2 To allow user to specify what values to subtract from modulation parameters (over-riding the default subtraction of the average).
11 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) fill gaps and holes in anatomical masks (now requires AFNI from 7 May, 2012)
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 10 Jul 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) let the user know whether 3dClustSim will be run
09 Jul 2012, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 5 (MODIFY) escape (unalias) every 'rm' command 09 Jul 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY) escape (unalias) every 'rm' command
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Use ArrowFields when datasets have large numbers of sub-bricks The switch is done automatically and is controlled with env: SUMA_ArrowFieldSelectorTrigger 06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV) SUMA_ArrowFieldSelectorTrigger set threshold for using ArrowFields For datasets with sub-bricks >= SUMA_ArrowFieldSelectorTrigger and arrow field is used to switch between sub-bricks
29 Jun 2012, RC Reynolds, @Install_RSFMRI_Motion_Group_Demo, level 2 (MINOR), type 1 (NEW_PROG) program is for installing demo of RSFMR on big and small motion groups 29 Jun 2012, RC Reynolds, prompt_user, level 1 (MICRO), type 2 (NEW_OPT) if MESSAGE is '-', read from stdin 29 Jun 2012, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY) moved ptaylor_install dependency from 'vastness' to 'install'
28 Jun 2012, ZS Saad, ROIgrow, level 2 (MINOR), type 2 (NEW_OPT) Added -insphere and -inbox options These options grow ROIs by finding nodes that fall inside a box or sphere of preset size around nodes in the original ROIs. 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)
27 Jun 2012, RC Reynolds, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) added -nzmedian, requested on message board
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 25 Jun 2012, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 6 (ENHANCE) added help for -factors and 3dANOVA3 -type 4 examples
22 Jun 2012, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) added commands 3dANOVA2 and 3dANOVA3; added option -factors Need to add help for -factors (i.e. for 3dANOVA3 -type 4).
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. 19 Jun 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -switch_cmode to allow switching how values map to colors This controls the 'Col' menu in SUMA's surface controller. 19 Jun 2012, RW Cox, 3dttest++, level 2 (MINOR), type 0 (GENERAL) Internal wildcard expansion with SHORT FORM '-set' options.
15 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_censor_extern 15 Jun 2012, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY) make num_dim violation a warning, because of mris_convert
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, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) warn users if married types and files do not seem to match 05 Jun 2012, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 4 (BUG_FIX) need to explicitly set DSET_BRICK_TYPE() on some systems
04 Jun 2012, ZS Saad, @Install_TSrestMovieDemo, level 1 (MICRO), type 1 (NEW_PROG) Demo script to make a resting state movie a la Daniel Margulies' 04 Jun 2012, ZS Saad, @Install_AfniRetinoDemo, level 1 (MICRO), type 1 (NEW_PROG) Demo script to download and run Retinotopy pipeline demo
03 Jun 2012, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE) for variable updates: actually show list if it is short enough 03 Jun 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) for resting state analysis, suggest -regress_censor_motion 0.2 Suggest a more strict limit for resting state than for task analysis.
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.
31 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Merged ptaylor's code changes into the distribution
30 May 2012, DR Glen, 3dinfo, 3drefit, level 2 (MINOR), type 5 (MODIFY) av_space option handling and orig/other space refitting 3dinfo reports view extension for -av_space instead of generic space view extension. 3drefit will warn if setting non-orig space on orig view data or orig space on tlrc view data.
25 May 2012, ZS Saad, SurfToSurf, level 1 (MICRO), type 4 (BUG_FIX) Improve auto-name generation and enabled output format specification 25 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE) display modified options and subject defaults
24 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Merger of changes in P. Taylor's code 24 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) csf_val and csf_fa options apply to linear solutions too
23 May 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Allow label-based selection for annotation files See function: process_NSD_labeltable(), now you can do something like: 3dcalc -a std.60.lh.aparc.a2009s.annot.niml.dset'' \ -expr 'step(a)' -prefix wm_lh_G_precentral.niml.dset 23 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -clust option, to allow 3dClustSim stuff to be used 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)
22 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added regress_bandpass and regress_mot_deriv (probably for resting state) 22 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) csf_val and csf_fa options for default values if B=0 less than gradient values
21 May 2012, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT) Made program output mapping info file for use with SurfToSurf Also made microscopic improvement to automatic dset name generation for -d set_map 21 May 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Made the script also port thickness data and take them to std. space 21 May 2012, ZS Saad, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Added -covariance option, turned off DOF setting for anything but pearson. See function THD_covariance() 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 21 May 2012, RW Cox, FDR calculations, level 1 (MICRO), type 3 (NEW_ENV) AFNI_NON_INDEPENDENT_FDR == YES --> like '-cdep' in 3dFDR. 21 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added the long-desired-but-not-so-needed -regress_stim_types option This allows users to specify -stim_times/_AM1/_AM2/_IM.
19 May 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) added help examples for resting state analysis 19 May 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) allow for auto-tcat of 1D inputs that are separated by spaces For E Demir to use in 3dDeconovolve.
17 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -donocov option When -covariates is used, -donocov says to also do the NO covariates analyses and tack them onto the end of the results -- for comparison fun
16 May 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY) do not ask for user input, even if centers are off by 80+ mm 16 May 2012, RC Reynolds, @GetAfniOrient, level 1 (MICRO), type 5 (MODIFY) suppress 3dinfo version text
15 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT) Added '[1dcat FF.1D]' syntax for sub-brick selections in 1D file This was added for the same reason '[count ...]' was added, and that is to allow for lengthy selection values. Dealing with selections of 100+ sub-bricks virtually guarantees some string limit is reached, somewhere. See 3dTcat -help for details 15 May 2012, ZS Saad, 1dRplot, level 1 (MICRO), type 2 (NEW_OPT) Added -load.Rdat to regenerate previous plot on command line
11 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) also output average censored per-TR motion
10 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) allow for a wider range of file names - handle case of more than 99 runs - look for files of the form *_rall.1D, as well as *.rall.1D 10 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) allow processing of more than 99 runs
08 May 2012, ZS Saad, count, level 2 (MINOR), type 2 (NEW_OPT) Added -form to count: count -form %c 49 130 08 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Code updates for P. Taylor's tractography 08 May 2012, ZS Saad, 3dSeg, level 2 (MINOR), type 4 (BUG_FIX) Fixed memory leak problem 08 May 2012, RW Cox, 1ddot, level 1 (MICRO), type 2 (NEW_OPT) Add -rank option to do Spearman correlations 08 May 2012, DR Glen, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) gen_space option to see generic space type for a dataset
07 May 2012, RW Cox, FIRdesign, level 1 (MICRO), type 1 (NEW_PROG) Finite Impulse Design filter design program -- for bandpass 07 May 2012, RW Cox, AFNI instacorr, level 1 (MICRO), type 5 (MODIFY) Modify treatment of Global Ort file If too short to allow for Ignore, then doesn't do Ignore on the Global Ort time series. Otherwise, does the initial Ignore on that input. The Help also reflects this change. In the past, it always did the Ignore on the Global Ort data, and if it couldn't, then it skipped them entirely. 07 May 2012, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 6 (ENHANCE) replaced THD_mask_erode with new THD_mask_erode_sym This change should make dilate and erosion operations symmetric. 07 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added weighted_enorm method for -collapse_cols; added -weight_vec 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. 07 May 2012, DR Glen, NIFTI input/output, level 2 (MINOR), type 5 (MODIFY) NIFTI qform/sform codes from generic space of template space qform and sform codes are set by string in generic space, not template space, of input dataset. For example, TT_N27 spaces will be marked for NIFTI output as TLRC. NIFTI data with any non-ORIG or ACPC space will be marked as an 'aligned' space in NIFTI with the sform and qform codes. Currently only TLRC/MNI/Aligned are supported spaces in NIFTI standard. 'aligned' space datasets will be interpreted as equivalent to TLRC view datasets. See AFNI_atlas_spaces.niml for space definitions that include generic space names. 07 May 2012, DR Glen, to3d, level 1 (MICRO), type 5 (MODIFY) Clearer warning for illegal transfer syntax 07 May 2012, DR Glen, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) out_space option to force output space for auto-talairached data
04 May 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added inverse distance measures to InstaCorr For the moment, those options are only accessible to usernames rwcox and ziad. Relevant functions are: THD_vectim_distance(), and THD_distance(). THD_distance() is not used at the moment, it would be from 3dLocalBistat once I get around to testing it. For now, its access from 3dLocalBistat is #if-ed out. 04 May 2012, RW Cox, 1dBport, level 1 (MICRO), type 2 (NEW_OPT) Add -quad option = linear and quadratic trend regressors 04 May 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 4 (BUG_FIX) submitting updates from Rayus Updates are in changelog.
03 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -backward_diff and -forward_diff Note, -backward_diff is the same as -derivative.
02 May 2012, RW Cox, coxplot, level 1 (MICRO), type 0 (GENERAL) More minor changes to timeseries plotting Rounded joins for lines drawn in 'new' mode. Use new mode for final rendering in plug_realtime.c (but not for realtime graphing). Etc. 02 May 2012, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) added AFNI_PATH_SPACES_OK, for input of datasets with spaces in path Added for V Roopchansingh.
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) 01 May 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE) allowed -ordered_stimuli and -max_consec, together Requested by Liat. 01 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) added -prefix option; added censor coloring to 1dplot commands 01 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) added -looks_like_AM
30 Apr 2012, RW Cox, 1dplot, level 1 (MICRO), type 0 (GENERAL) Add anti-aliasing rendering to X11 drawing as well. Set AFNI_1DPLOT_RENDEROLD to YES to turn this feature off (but why?). 30 Apr 2012, RC Reynolds, afni_restproc.py, level 3 (MAJOR), type 1 (NEW_PROG) this program is by Rayus Kuplicki, please contact him for information
27 Apr 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added percentile thresholding to AFNI's interface Relevant functions: flush_vinfo_sort(); flush_3Dview_sort(); get_3Dview_sort(); AFNI_thresh_from_percentile() Relevant structure variables: cont_perc_thr in Three_D_View; th_sort, N_th_sort, th_sortid in AFNI_view_info; Feature also accessible from plugout_drive with: SET_FUNC_PERCENTILE +/- 27 Apr 2012, RW Cox, 3dANOVA and 3dRegANA, level 1 (MICRO), type 0 (GENERAL) Modified to use a random SUFFIX for temp filenames To avoid conflict when running 2+ copies in the same directory. Per the request of Tom Holroyd. 27 Apr 2012, RW Cox, 1dplot, level 1 (MICRO), type 0 (GENERAL) Modify rendering of images (jpeg, png) to look nicer 27 Apr 2012, RC Reynolds, 3dmask_tool, level 3 (MAJOR), type 1 (NEW_PROG) a program to manipulate mask datasets
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 26 Apr 2012, RW Cox, 3dLocalBistat, level 2 (MINOR), type 2 (NEW_OPT) Allow 1 volume vs. multi-volume; Add slope options
25 Apr 2012, RW Cox, 3dNormalityTest, level 1 (MICRO), type 2 (NEW_OPT) Add -pval option, to get a 'pure' p-value out
24 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Can read .niml.tract files as DOs. Nothing too fancy yet Tractography files are loaded and handled like any DO. See function SUMA_DrawTractDO(). 24 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Wrote TrackIO.[ch] to handle tractography data I/O. All changes are under ptaylor/ . New tract format is in NIML. See functions in TrackIO.h for details. 24 Apr 2012, ZS Saad, 3dTrackID, level 2 (MINOR), type 5 (MODIFY) Modified 3dTrackID to make use of new track I/O functions. 24 Apr 2012, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT) Add censor stuff to 1dplot, for Colm 24 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) if surface data with generic prefix, append surf-type suffix Done to fix ANOVA commands on surface. Thanks to R Ray for bringing this up.
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.
17 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) added atlas/ROI label use with <> range selectors (MCW_get_angle_range)
16 Apr 2012, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY) New convenience functions for I/O SUMA_AddDsetIndexCol(), SUMA_CreateFullDsetPointer, and macro SUMA_DSET_NAME_CHECK Improved name parsing and format guessing. 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) More I/T selector linkage modes. 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Show data value at crosshair directly in display See SUMA_UpdateCrossHairNodeLabelFieldForSO(), SUMA_FormNodeValFieldStrings(), and SUMA_UpdateNodeValField() 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Better handling on multiline centering for display in viewer window. 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) New option to control which node-based DOs are displayed. See SUMA's interactive help on 'Ctrl+p' for details. 16 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY) Created ptaylor/ under src/ to include Paul Taylor's code contributions To compile all of Paul's programs: cd src/ptaylor; make all or from src/ make ptaylor_all Added macros AFNI_3D_to_1D_index and AFNI_1D_to_3D_index in 3ddata.h 16 Apr 2012, ZS Saad, SurfaceMetrics, level 2 (MINOR), type 5 (MODIFY) Improved output format and added Displayable Objects to output. 16 Apr 2012, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) Added -closest_possible For allowing the substitution of the projection result with the closest node that could be found along any direction. See changes to SUMA_GetM2M_NN() 16 Apr 2012, ZS Saad, SampBias, level 2 (MINOR), type 5 (MODIFY) Improved I/O 16 Apr 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -do_draw_mask to restrict where node-based DOs are shown 16 Apr 2012, ZS Saad, plugout_drive, level 1 (MICRO), type 5 (MODIFY) Cosmetic error message handling to help debugging SLaconte problems 16 Apr 2012, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY) Added new help features to bunch of programs 1dCorrelate, 1dTsort, 1ddot, 3dANOVA*, 1dplot, 3dAutobox, cat_matvec, waver 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. 16 Apr 2012, ZS Saad, 1dTsort, level 1 (MICRO), type 2 (NEW_OPT) Added -imode to return the mode of 1D file content. 16 Apr 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -regress_bandpass, for bandpass filtering via regression
13 Apr 2012, RC Reynolds, @radial_correlate.py, level 1 (MICRO), type 6 (ENHANCE) accept +tlrc datasets
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
08 Apr 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE) -ordered_stimuli now takes labels
05 Apr 2012, RW Cox, 3dTnorm, level 2 (MINOR), type 1 (NEW_PROG) Normalize each time series in a dataset Like 1dnorm for 3D+time datasets 05 Apr 2012, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add -zcount option: count number of zero values in a voxel
04 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) if prefix shows STORAGE_UNDEFINED, use BRIK only if not potential surface
03 Apr 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL) dmBLOCK now defaults to peak=0 ==> variable amplitude Former behavior is now achieved with dmBLOCK(1) ==> fixed amplitude. Also, the peak variable amplitude is now 1, rather than some annoying value that means nothin to nobody nohow. 03 Apr 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY) always print the name of the mask dataset in use (via GUI or env)
02 Apr 2012, RW Cox, Lion build, level 1 (MICRO), type 0 (GENERAL) Modify install process to include useful netpbm program binaries The stuff that imseq.c uses to write images out (GIF, TIFF, PNG, BMP), so that fink is not required. Done via Makefile macro EXTRA_INSTALL_COMMANDS and copying all files in directory EXTRAPROGS to the output binaries. 02 Apr 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL) Add MIONN() function to repertoire (negative MION)
30 Mar 2012, RC Reynolds, plug_realtime, level 1 (MICRO), type 5 (MODIFY) let user know when AFNI_REALTIME_Mask_Dset is applied 30 Mar 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) added option -inweight Added for S Horovitz and S Tinaz.
22 Mar 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Improve display of node-based DOs. ctrl+p for showing subset of objects. Node-based DOs overwhelm the display. Ctrl+p allows one to show DOs only around the selected node, or just at it. See also DriveSuma's -do_mask_mode option. 22 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Add values at node to the display. This involved an improvement to the centering of text so that one can center each line in a paragraph 22 Mar 2012, ZS Saad, @Spharm.examples, level 2 (MINOR), type 5 (MODIFY) Improvements to the script to make it work with new programe versions. It will now download its own data for demo purporses. 22 Mar 2012, ZS Saad, SurfaceMetrics, level 1 (MICRO), type 2 (NEW_OPT) Now outputs NIML dsets and Displayable objects for certain metrics 22 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE) apply AFNI_REALTIME_SHOW_TIMES in non-RT feedback case 22 Mar 2012, RC Reynolds, Dimon, level 1 (MICRO), type 6 (ENHANCE) if RT comm fails with afni, show iochan_error_string() It occasionally fails at TR=0.125 s.
21 Mar 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE) look for more motion files; minor changes to output format 21 Mar 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) use run_lengths for TR list; removed path from external motion file 21 Mar 2012, RC Reynolds, 3dcalc, level 1 (MICRO), type 6 (ENHANCE) added -help description to -help output To get apsearch to enable completion of -help option.
19 Mar 2012, RW Cox, Makefiles, level 1 (MICRO), type 0 (GENERAL) Remove -O3 and -ffast-math and -ftree-vectorize from all gcc cases Too many problems on Lion with -O3 make me suspicious of aggressive optimization in general.
15 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE) added AFNI_REALTIME_Mask_Dset for per-run control over Mask Also added some missing vars to README.environment. Done for J Evans.
14 Mar 2012, RW Cox, AFNI package, level 1 (MICRO), type 0 (GENERAL) Add Makefile for Mac OS X 10.7 == Lion No thanks to Apple, by the way -- breaking OpenMP -- what a bunch of maroons. 14 Mar 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -num_chan and -max_quiet_trs; default sleep = 1.1*TR, max of 2 Added for J Evans and V Roopchansingh. 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.
13 Mar 2012, RC Reynolds, lib_qt_gui.py, level 1 (MICRO), type 5 (MODIFY) has main, so added trivial -help option
12 Mar 2012, RC Reynolds, @SUMA_AlignToExperiment, level 1 (MICRO), type 2 (NEW_OPT) added -overwrite_resp, so that processing does not have to stop and wait Also, used 'find' grab *.nii, to fix the failure reported by R Ray. Forgot to put this in with the afni_proc.py change...
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, RW Cox, many, level 1 (MICRO), type 0 (GENERAL) Many small changes to fix problems caught with the llvm compiler. 07 Mar 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) existing package and install dir no longer required for -defaults 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. 06 Mar 2012, RW Cox, 3dNormalityTest, level 2 (MINOR), type 1 (NEW_PROG) Test voxel values for normality (Gaussianity). Uses the Anderson-Darling test. 06 Mar 2012, RC Reynolds, uber_subject.py, level 1 (MICRO), type 5 (MODIFY) move nokia help to -help_install_nokia (since it is not recommended)
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, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT) Added option auto-completion for AFNI's programs for csh users The implementation of this feature is via apsearch. In particular, apsearch -update_all_afni_help now creates the necessary commands for csh's complete program to know about available options. See apsearch -help for details. This was done in conjunction with Brian Pittman. 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. 05 Mar 2012, RC Reynolds, uber_proc.py, level 1 (MICRO), type 5 (MODIFY) trivially apply -help option, for apsearch 05 Mar 2012, RC Reynolds, apsearch, level 1 (MICRO), type 5 (MODIFY) do not set shell variables
02 Mar 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) fixed $runs in multi-run ricor Thanks to I Mukai 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. 01 Mar 2012, RW Cox, 1dBport, level 2 (MINOR), type 2 (NEW_OPT) Several things to keep Rick happy Option '-band fbot ftop' can now be used more than once. New option '-nozero' means to NOT include the 0 frequency. New option '-invert' means to calculate the frequency indexes to remove from the various '-band' options, then invert them to KEEP only those frequencies instead. That is, only the frequencies NOT specified via '-band' will be output in the resultant 1D file.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added option to use html viewer for WAMI results. This is to allow users to click on a URL if one is available for a certain atlas result. For now the display is very crude and only accessible with -DWEBBY_WAMI=YES. 29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added 'ctrl+W' that allows saving results from interactive correlations. This allows for convenient saving of interactively created datasets such as those from single-subject, or group correlation maps in resting state.
27 Feb 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allow on the fly definition of standard meshes with -i ld120, for example. 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, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) made a little more intelligent, e.g. make one backup by default Note: can run this without any existing AFNI binaries, e.g. @update.afni.binaries -bindir ~/abin -package linux_openmotif 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, general, level 3 (MAJOR), type 5 (MODIFY) I/O library for R now can use AFNI's c library. This new functionality allows the use a variety of formats both surface and volume-based for reading to and writing from R. 3dMEMA can use this new functionality with option -cio 24 Feb 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 4 (BUG_FIX) Added number of volume registration regressors to -ort_adjust 24 Feb 2012, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Options -val_diff and -sval_diff to compare values in 2 dsets. 24 Feb 2012, ZS Saad, 3dMEMA, level 2 (MINOR), type 2 (NEW_OPT) 3dMEMA can now handle surface-based data It makes use of the new I/O functions that use AFNI's C-library. 24 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY) added -moderate_mask, fixed -extreme_mask help Thanks to R Kuplicki for reporting the help inconsistency.
23 Feb 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY) Enable 'bigthree' mode for color pbar If AFNI_PBAR_THREE is YES, the color pbar in the AFNI GUI (but not the renderer) will start in 'bigthree' mode, with 3 panes -- the colorscale in the middle one, and the upper and lower panes adjustable to allow for scaling that is not symmetrical.
22 Feb 2012, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) Compute the mode of ROI voxels, see -mode and -nzmode 22 Feb 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) moved GLOBAL_browser def from afni.h to thd_ttatlas_query.c - declared in TTQ.h - deleted #include thd_atlas.h from most .c files - #include thd_atlas.h in mrilib.h 22 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -randomize_trs and -seed Affected 1d_tool.py, afni_util.py, lib_afni1D.py and lib_textdata.py.
21 Feb 2012, RW Cox, 3dAutobox, level 1 (MICRO), type 2 (NEW_OPT) Add -npad option, for Larry Frank 21 Feb 2012, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE) if destination directory is not writable, let the user know 21 Feb 2012, DR Glen, whereami, level 4 (SUPER), type 2 (NEW_OPT) Web-based access atlases available Able to query web atlases from whereami and open webpages Support starting with rat brain atlas from Elsevier's BrainNavigator
17 Feb 2012, RW Cox, debugtrace.h, level 1 (MICRO), type 5 (MODIFY) Add printout of 'from' and 'to' information on ENTRY/RETURN macros Also patched up a missing ENTRY macro in new_MCW_optmenu() in bbox.c, that SOMEONE (who shall go un-named) criminally forgot when patching the code for LessTif compatibility.
16 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) more quick termination updates - added -max_images - do not init vol search state to 2, would limit volumes to 40 - include fl_start in no_wait test - look for new vol worth of images, but no volume match
14 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE) release version 1.0: help, copy tables, scripts imply -no_gui 14 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY) if -no_wait, terminate on volume_match failure For F Ye.
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. 10 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE) added 'paired' toggle box to GUI 10 Feb 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 5 (MODIFY) tiny help update, as enforced by H Jo 10 Feb 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY) make tcat files optional; apply prefix to 'basic' commands in driver 10 Feb 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -check_results_dir for Z Saad Also, changed -tcat_outlier_warn_limit to -tcat_preSS_warn_limit.
09 Feb 2012, ZS Saad, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT) Added -sdata, making 3dSurf2Vol compatible with multitude of surface dsets
08 Feb 2012, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL) Add ability to flip colors in a discrete paned pbar And a 'Flip Colors' button to do so.
07 Feb 2012, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT) Added -out option to handle output in various formats. Also added -func ALL option. 07 Feb 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -bkg_col and -autorecord options 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, suma, level 2 (MINOR), type 2 (NEW_OPT) Added automatic sub-brick selection matching IxT in interface Also see corresponding env var: SUMA_IxT_LinkMode 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. 06 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE) added -no_wait option: never wait for new data Also, suppress new glob warnings. Done for F Ye and others. 06 Feb 2012, RC Reynolds, to3d, level 1 (MICRO), type 5 (MODIFY) tiny help update, as enforced by D Glen 06 Feb 2012, RC Reynolds, 3dsvm, level 1 (MICRO), type 5 (MODIFY) applied Makefile.INCLUDE updates for J Lisinski and S LaConte
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.
02 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE) added basic 3dMEMA capabilities This affected afni_util.py, ask_me.py, gui_uber_ttest.py, lib_qt_gui.py lib_subjects.py, lib_uber_ttest.py, uber_subject.py, uber_ttest.py.
01 Feb 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) check for pre-steady state outlier counts Added option -tcat_outlier_warn_limit. 01 Feb 2012, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 6 (ENHANCE) check for pre-steady state outlier warnings
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. 31 Jan 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) look for aligned anat _al_junk/keep 31 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_apply_ricor
30 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) ricor block: no longer apply in later 3dDeconvolve The regressors for slice #0 from the ricor block were being applied in the final regression (to remove motion) for consistency in degrees of freedom. But we might rather not do that, particularly since DOF are not important when proceeding with just correlation coefficients. 30 Jan 2012, RC Reynolds, uber_ttest.py, level 1 (MICRO), type 5 (MODIFY) all python files use '/usr/bin/env python' instead of '/usr/bin/python' modified afni_base.py, gui_uber_align_test.py, gui_uber_subj.py, uber_skel.py, @DoPerRoi.py, gui_uber_skel.py, gui_uber_ttest.py, uber_ttest.py
28 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) updates for surf analysis of subject FT under AFNI_data6 - added -atlas_followers to @SUMA_AlignToExperiment - if surf analysis: no scaling mask (e.g. extents) - updated help example #8 for surf analysis of AFNI_data6 subject FT 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.
26 Jan 2012, ZS Saad, 3dinfill, level 2 (MINOR), type 1 (NEW_PROG) Fills holes in a volume based on neighboring values This program is a wrapper to function SUMA_VolumeInFill. Written in response to a query by Mike Beauchamp.
25 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX) back out overzealous -quit changes for now
24 Jan 2012, ZS Saad, SurfExtrema, level 2 (MINOR), type 1 (NEW_PROG) Finds nodes that are local extrema on the surface. Program in response to request by Daniel Margulies
23 Jan 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allowed addition of 'R' or 'L' when jumping to a node. This make DriveSuma work well with node indices that are specified for two hemispheres as is done in the batch mode of 3dGroupInCorr. This applies to both suma and DriveSuma 23 Jan 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added -ld and -no_ld options @SUMA_Make_Spec_FS by default now runs MapIcosahedron at two ld values. 23 Jan 2012, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Added -atlas_followers Automatically bring along atlas datasets under -surf_anat's directory. 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.
20 Jan 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added -h_web, and -Vname= to all C command-line programs. See also apsearch -web_prog_help option 20 Jan 2012, ZS Saad, afni, level 1 (MICRO), type 5 (MODIFY) Trim dset names to keep them readable in plugin dataset selector buttons See function TrimString() and how it is used in PLUG_finalize_dataset_CB() 20 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 5 (MODIFY) mri_read_dicom: if there is no VALID vrCode, skip explicitVR Done for Chad N.
19 Jan 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Allow definition of DO on the fly with -fixed_do, -mobile_do. See DriveAfni -help and suma -help_nido 19 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY) made -quit more aggressive
18 Jan 2012, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT) -s option to test string NI elements 18 Jan 2012, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 2 (NEW_OPT) -closest_* options to create find nodes that fall closest to XYZ locations 18 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 3 (NEW_ENV) SUMA_Position_Original for controlling initial window position. Use suma -update_env ; to update env file, then look for env SUMA_Position_Original for help and default value. 18 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) force anat variable (and children) to be in AFNI format after 3dcopy Appropriate, and for compatibility with an afni_name.pv change.
17 Jan 2012, ZS Saad, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Allowed BATCH mode to work on surfaces. 17 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY) -gert_create_dataset now implies -GERT_Reco and -quit For Ziad and Daniel.
13 Jan 2012, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Options -pre and -app help in creating filenames regarding of type
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, ZS Saad, afni-general, level 1 (MICRO), type 5 (MODIFY) Added copying of label table and atlas point lists to aux copying function See functions THD_copy_labeltable_atr and THD_copy_datablock_auxdata for details. 11 Jan 2012, ZS Saad, 3drefit, level 1 (MICRO), type 2 (NEW_OPT) Added -copytables to copy label tables and atlas point lists 11 Jan 2012, ZS Saad, 3dROIstats, level 1 (MICRO), type 5 (MODIFY) Use ROI labels in output if label tables or atlas point lists are present 11 Jan 2012, RW Cox, many programs, level 1 (MICRO), type 0 (GENERAL) Print WARNING message if '-polort A' is used where not allowed This is the Inati's fault. 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.
10 Jan 2012, ZS Saad, 3dTagalign, level 1 (MICRO), type 2 (NEW_OPT) Added interpolation options. 10 Jan 2012, RW Cox, 1dBport, level 2 (MINOR), type 1 (NEW_PROG) Generates sin/cos waveforms for bandpass-via-regression
09 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 2 (NEW_OPT) Added -setenv to all SUMA programs 09 Jan 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -setSUMAenv,-N_fore_smooth, and -N_final_smooth
06 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT) Added -keep_separate to allow for another way to split ROIs
04 Jan 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Automatically add an Atlas to whereami list if encountered in the session 04 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT) Added -nodelist_with_ROIval to facilitate splitting ROIs 04 Jan 2012, ZS Saad, @Atlasize, level 1 (MICRO), type 2 (NEW_OPT) Allow for delimiters in keys file and handle names with spaces Similar additions are made to @MakeLabelTable 04 Jan 2012, RW Cox, 1dsvd, level 1 (MICRO), type 5 (MODIFY) Add percent ability to -nev option That is, the ability to output (via -1Dleft) the set of vectors that make up the first 'n' percent of the column space.
03 Jan 2012, RW Cox, THD_dset_in_session, level 1 (MICRO), type 5 (MODIFY) Alter FIND_PREFIX to strip off '+view' if present.
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.) 30 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Simplified how afni handles custom group or single-subject atlases By default, SessionAtlases and AFNI_SUPP_ATLAS_DIR/CustomAtlases.niml are added to the atlas list for whereami queries. 30 Dec 2011, ZS Saad, @MakeLabelTable, level 2 (MINOR), type 2 (NEW_OPT) Improved @MakeLabelTable's creation of ATLAS niml files 30 Dec 2011, ZS Saad, @Atlasize, level 2 (MINOR), type 1 (NEW_PROG) A convenience script to turn a dataset to an atlas The script makes it easy to create a group atlas or a single-subject atlas and place them automatically in a location that AFNI recognizes making them available to the user without bothering with too many environment variable settings. 30 Dec 2011, ZS Saad, @AfniEnv, level 2 (MINOR), type 1 (NEW_PROG) A convenience script to automatically edit .afnirc 30 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Numerous new options to 3dinfo, including checks for dset presence on disk
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
23 Dec 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Allow user to append a string to the overlay label Via environment AFNI_IMAGE_LABEL_STRING or by a new item on the intensity bar popup menu in the GUI -- the latter takes precendence. This is Ziad's Xmas present.
22 Dec 2011, RW Cox, mycat, level 1 (MICRO), type 1 (NEW_PROG) Minor program to be sort of like 'cat' but un-Microsofts files. 22 Dec 2011, RW Cox, afni_fgets, level 1 (MICRO), type 5 (MODIFY) Modified to use system fgets if file pointer is a ttty 22 Dec 2011, RW Cox, afni realtime plugin, level 1 (MICRO), type 3 (NEW_ENV) AFNI_REALTIME_External_Dataset environment variable Lets the realtime user (let's call her/him 'CC') specify an external dataset to be used as the registation base. CC doesn't have to use a dataset that is in the cwd, unlike the plugin's GUI selector. Nor does the setting of this environment variable affect the plugin's GUI.
21 Dec 2011, RW Cox, afni_fgets, level 1 (MICRO), type 5 (MODIFY) Modify to use system fgets for stdin
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) SUMA now allows for direct recording to disk. See SUMA's ctrl+h for key ctrl+R for details. Related environment variable is SUMA_AutoRecordPrefix. 20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) SUMA now displays area labels in the viewer, F9 key toggles it See SUMA's ctrl+h output in the section for F9 Related environment variable is SUMA_ShowLabelsAtCrossHair. 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. 20 Dec 2011, ZS Saad, 3dUpsample, level 2 (MINOR), type 2 (NEW_OPT) Allow for upsampling to go to 11 (actually 320) and control output datum 20 Dec 2011, RW Cox, fgets, level 1 (MICRO), type 0 (GENERAL) Replace (mostly) fgets with afni_fgets Recognizes CR and CR+LF and LF+CR as line enders, not just LF like the standard Unix library function -- these Microsofties are killing me. 20 Dec 2011, RW Cox, fdrval, level 1 (MICRO), type 5 (MODIFY) Add -inverse (AKA -qinput) option Allows user to compute the threshold, given the q-value. 20 Dec 2011, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY) Add debug output to thd_table.c To help me (and users) figure out what might be wrong with a covariates table. Also applies to 3dGroupInCorr
19 Dec 2011, RW Cox, THD_patch_brickim, level 1 (MICRO), type 5 (MODIFY) Modify to set zero dataset grids spacings to a nonzero value In the dataset struct itself, that is, not just the brick image structs.
16 Dec 2011, RW Cox, 3dLSS, level 1 (MICRO), type 0 (GENERAL) Added -nodata option, and fleshed out the help with an example.
15 Dec 2011, RW Cox, 3dLSS, level 1 (MICRO), type 1 (NEW_PROG) 3dLSS implement LS-S regression As described in Mumford, Turner, Asby, and Poldrack, NeuroImage 2011. See 3dLSS -help for more info.
13 Dec 2011, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) -init_xform to allow for an initial transformation of -surf_anat 13 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) -same_* options return information about dset pairs 13 Dec 2011, ZS Saad, plugout_drive, level 1 (MICRO), type 4 (BUG_FIX) AFNI_drive_switch_* functions discriminated against short prefixes.
12 Dec 2011, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Small improvements and addition of logging option of search results See -apsearch_log_file option for details. Logging is only enabled if AFNI_LOG_BEST_PROG_OPTION is set to YES. 12 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Slice displays can now show atlas labels in addition to slice location The displays are turned on by right-clicking on the slice viewer's color bar and then setting the 'Label' to something other than 'OFF' See isqCR_getlabel, ISQ_getlabel, and AFNI_get_dset_val_label in code 12 Dec 2011, ZS Saad, @global_parse, level 2 (MINOR), type 1 (NEW_PROG) Script to simplify support of global options such as h_find from scripts
09 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV) SUMA_DoNotSendStates restricts certain surfaces from getting sent to suma. 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, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added atlas creation of aseg, aparc+aseg, in addition to aparc.a200* See whereami's example 3 for how to extract ROIs from FreeSurfer atlases. 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.
06 Dec 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT) -stdin for input More tweaking of search distances and a battery of tests to help decide if tweak is in the right direction. 06 Dec 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 0 (GENERAL) Allow runs with -polort ONLY (no other regression model)
05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added -h_view to all C command-line programs. See also apsearch -view_prog_help option 05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 3 (NEW_ENV) AFNI_GUI_EDITOR controls user's preferred text editor. See apsearch -afni_text_editor.
02 Dec 2011, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) -XYZscale is added to scale the coordinates of a surface Surface that are not in mm coordinates can look pretty bad in SUMA. This scaling option can be used to easily change coordinates from cm to mm for example. 02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added 'Save' button to suma text info windows 02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 3 (NEW_ENV) SUMA_NodeCoordsUnits allows the specification of node coord. units 02 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 4 (BUG_FIX) Wrote SOLARIS_strcasestr to replace missing strcasestr on SOLARIS 02 Dec 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) Add -ortvec option (to appease the Inati) Lets the pitiful user add multiple baseline (i.e., ort) vectors from a single file.
01 Dec 2011, RW Cox, p2t, level 1 (MICRO), type 0 (GENERAL) Remove this program from AFNI binary distributions
30 Nov 2011, ZS Saad, ConvertDset, level 1 (MICRO), type 2 (NEW_OPT) -pad_to_node 0 now padds output dset to max node in input dset
29 Nov 2011, ZS Saad, @clean_help_dir, level 1 (MICRO), type 1 (NEW_PROG) Removes redundant help files from the afni help directory. 29 Nov 2011, ZS Saad, @DeblankFileNames, level 1 (MICRO), type 1 (NEW_PROG) Replaces spaces in filenames with_something_less_annoying.
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.
25 Nov 2011, ZS Saad, to3d, level 1 (MICRO), type 2 (NEW_OPT) Added -quit_on_err Keeps to3d from going in interactive mode in case of error. 25 Nov 2011, ZS Saad, Dimon, level 1 (MICRO), type 2 (NEW_OPT) Added -gert_quit_on_err Passes -quit_on_err option to to3d.
22 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -h_find as a global option afni -help now outputs information about 'Global options' 22 Nov 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) allow for passing variables directly, not via -svar
21 Nov 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT) Added -all_opts to show all options for a program 21 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -all_opts as a global option The option is the equivalent of running apsearch -all_opts for a certain program. 21 Nov 2011, RC Reynolds, quick.alpha.vals.py, level 2 (MINOR), type 1 (NEW_PROG) a very simple program to tabulate the output from slow_surf_clustsim.py This ought to be improved, but at least it is now distributed... 21 Nov 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE) small update to help text 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, ZS Saad, apsearch, level 2 (MINOR), type 1 (NEW_PROG) This is a program to test approximate string matching functions The program is best described by its help output. It is meant to quickly test the behavior of the approx* functions in thd_ttatlas_query.c where approximate string matching will be useful is easily specifying an atlas areas by name. Another useful offshoot is the function: suggest_best_prog_option which can easily be called right after a command-line parsing error message is displayed. For example, in apsearch I have the following: { /* bad news in tennis shoes */ fprintf(stderr,"** Error %s: bad option %s\n", argv[0], argv[iarg]); suggest_best_prog_option(argv[0], argv[iarg]); return 1; } So all is needed to retrofit an old program is the suggest function. That function will do nothing if environment variable AFNI_NO_OPTION_HINT is set. To use suggest_best_prog_option from a script, use: apsearch -popt `basnemane $0` -word ARG 17 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) If AFNI_NO_OPTION_HINT, don't bother with helpful suggestions 17 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV) Added threshold locking capability under the 'Lock' menu 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, dicom_hinfo, level 1 (MICRO), type 0 (GENERAL) Minor edits, mostly to the help. 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 15 Nov 2011, RW Cox, dicom_hinfo, level 2 (MINOR), type 1 (NEW_PROG) For printing out info from lots of DICOM files For each file input, prints 1 line with the values of only the desired tags. The goal is to be helpful in figuring out which files go together. See Example #2 in the help output for such a case.
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. 10 Nov 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 2 (NEW_OPT) Add ExtraSet option That is, to correlate seeds from the TimeSeries dataset with voxel data from the ExtraSet dataset. Ziad asked for something like this, so here it is.
09 Nov 2011, RW Cox, 3dUndump, level 2 (MINOR), type 2 (NEW_OPT) Add -ROImask option To put values into locations defined by a mask dataset. 09 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) -surf_blur_fwhm is no longer valid, please use -blur_size
08 Nov 2011, RW Cox, afni, level 1 (MICRO), type 3 (NEW_ENV) AFNI_IMAGE_COLORANGLE Set this to 360 to get the 'Colr' image to be a full circle colormap. 08 Nov 2011, RC Reynolds, adwarp, level 1 (MICRO), type 6 (ENHANCE) added a help example for writing anat+tlrc.BRIK
07 Nov 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY) No -iresp or -sresp for dmBLOCK Also, change defintion of 'near-duplicate' times from 0.05*TR to 0.50*TR 07 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -blur_to_fwhm and -blur_opts_B2FW Added for E Nelson and J Jarcho. 07 Nov 2011, DR Glen, lost last character in sub-brick labels, level 2 (MINOR), type 4 (BUG_FIX) Fixed miscount of characters 07 Nov 2011, DR Glen, deobliquing, level 2 (MINOR), type 5 (MODIFY) More programs lose original data obliquity 3drefit, 3dWarp, 3daxialize, 3dZcutup, 3dCM, 3dZregrid added to the list of programs
04 Nov 2011, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 6 (ENHANCE) added 'mode' mapping function Requested by R Mruczek. Also done for Z Puckett.
03 Nov 2011, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 2 (NEW_OPT) added -prefix option; allow for 3dAllin failures; copy time info Updates by N Mei and A Messinger. 03 Nov 2011, DR Glen, longer sub-brick labels, level 2 (MINOR), type 5 (MODIFY) Allow sub-brick labels to be up to 63 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 02 Nov 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) added out.TENT_warn.txt to warning file review 02 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) if using TENT, run 'timing_tool.py -warn_tr_stats' Warnings are also saved in out.TENT_warn.txt. 02 Nov 2011, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE) allow -save_file_list to apply even with -infile_list
31 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_tr_stats and -warn_tr_stats options
26 Oct 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Made SUMA hide overlay from SUMA whenever 'See Overlay' is off in AFNI 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.
25 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE) process married files with current operations 1. AfniMarriedTiming inherits from AfniData (instead of local copies) 2. add all AfniTiming methods to AfniMarriedTiming (as married timing) 3. rename AfniMarriedTiming back to AfniTiming (but now married) 25 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) look for more file name variants, including with '_' separators Added for J Weisberg.
20 Oct 2011, RC Reynolds, afni_general, level 2 (MINOR), type 5 (MODIFY) changed most resampling programs to deoblique inputs upon read THD_open*_dataset() was followed by THD_make_cardinal(). modified: 3dresample, 3dfractionize, 3drotate, adwarp, 3dLRflip 3dZeropad, 3dZcat, 3dAutobox not (yet) modified: 3dWarp(Drive), 3dAllineate
19 Oct 2011, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE) can read/write ascii COMPLEX64, COMPLEX128, RGB24 Requested by H Breman, J Mulders and N Schmansky. 19 Oct 2011, RC Reynolds, @2dwarper.Allin, level 1 (MICRO), type 2 (NEW_OPT) added a -mask option Added for A Messinger.
18 Oct 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -available_npb* options to suggest available port blocks 18 Oct 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added blur size control; removed requirement of stim timing files 18 Oct 2011, RC Reynolds, @radial_correlate, level 1 (MICRO), type 6 (ENHANCE) require enough volumes per dataset, store file name correspondence
17 Oct 2011, RW Cox, 3dhistog, level 1 (MICRO), type 5 (MODIFY) removed DOS ctrl-M's in file, they screwed things up for compiling 17 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) added -help for new -surf_* options, along with example #8 17 Oct 2011, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY) abin now has subdir (funstuff), so change 'mv' to 'rsync'
14 Oct 2011, ZS Saad, afni-general, level 2 (MINOR), type 0 (GENERAL) Improvements of atlas handling in whereami and afni 1- In addition to loading atlas specs from environment variable AFNI_SUPP_ATLAS, AFNI will automatically search for a file named SessionAtlases.niml which is created with @MakeLabelTable. 2- AFNI will check if a viewed dataset is an atlas and will automatically add it to the atlas list. It will also show the label at the cross-hair location. New functions of interest: get_Atlas_ByDsetID, is_Dset_Atlasy, label_table_to_atlas_point_list, is_identity_xform_chain 14 Oct 2011, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) now processes surface data - added 'surf' processing block, and corresponding '-surf_*' options: -surf_anat, -surf_spec, -surf_anat_aligned, -surf_anat_has_skull, -surf_A, -surf_B, -surf_blur_fwhm - compute errts and TSNR by default (had required option or blur est) 14 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) allow modest handling of surface results 14 Oct 2011, RC Reynolds, uber_subject.py, level 1 (MICRO), type 6 (ENHANCE) small -help_install update
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.
12 Oct 2011, RW Cox, NIML library, level 1 (MICRO), type 0 (GENERAL) Extend printout of floats to higher precision
11 Oct 2011, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) Added support for NIFTI datasets 11 Oct 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Added new options for extracting field values in scripts
07 Oct 2011, RW Cox, afni, level 1 (MICRO), type 0 (GENERAL) Move splashes, faces, and poems to funstuff/ subdirectory funstuff/ is now a sub-directory of the binary install directory. 07 Oct 2011, RW Cox, 1dTsort, level 1 (MICRO), type 0 (GENERAL) Add -col option, to sort on just one column.
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
04 Oct 2011, ZS Saad, GroupAna, level 2 (MINOR), type 2 (NEW_OPT) Added support for writing NIML files as output This also required writing a few new matlab functions such as BrikInfo_2_niml_writesimple. 04 Oct 2011, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT) Added -min_nodes option 04 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) changed basic script outputs - added 'max censored displacement', 'final anat dset' and 'final voxel resolution' to basic script - removed 'num stim files found' 04 Oct 2011, RC Reynolds, to3d, level 1 (MICRO), type 5 (MODIFY) explicitly warn about illegal '/' characters in output filename 04 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -anat_has_skull option
03 Oct 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -censor_infile (e.g. to remove TRs from motion params) Added for N Adleman. 03 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) changed default polort time back to TR*NT, to match 3dDeconvolve 03 Oct 2011, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) update ADN_ONE_STEP to ten million, allowing that many output sub-bricks This affects programs like 3dbucket, when the output has many volumes. Done for HJ Jo, J Gonzalez-Castillo, M Robinson.
22 Sep 2011, RC Reynolds, uber_ttest.py, level 3 (MAJOR), type 1 (NEW_PROG) a graphical program for running either 3dttest++ or 3dMEMA Still under destruction. 22 Sep 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY) altered spacing and made other minor changes 22 Sep 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) added check_for_file and for_dset, updated find_x_mat, enorm, view_stats 22 Sep 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE) various updates - updated quotize_list - added nuke_final_whitespace, flist_to_table_pieces, get_ids_from_dsets 22 Sep 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY) moved get_def_tool_path to library
21 Sep 2011, RW Cox, 3dTshift, level 1 (MICRO), type 2 (NEW_OPT) Add -voxshift option 21 Sep 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add -2sided option
13 Sep 2011, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT) Added non_zero and count options 13 Sep 2011, DR Glen, whereami, level 1 (MICRO), type 4 (BUG_FIX) Added trivial ability to invert identity transformation
07 Sep 2011, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY) added @radial_correlate to the install scripts (forgot earlier)
06 Sep 2011, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) added -fast option, short for: -sleep_init 50 -sleep_vol 50 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, @radial_correlate, level 2 (MINOR), type 1 (NEW_PROG) compute voxelwise EPI correlations with local spherical averages 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).
31 Aug 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) if censoring motion or outliers, add options to gen_ss_r command
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.
26 Aug 2011, RW Cox, afni Clusterize, level 1 (MICRO), type 0 (GENERAL) Modify to print out 3dclust and whereami commands when used Per the suggestion of Andy Connolly of Dartmouth College. 26 Aug 2011, RW Cox, 3dclust, level 1 (MICRO), type 2 (NEW_OPT) add -savemask option
19 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 5 (MODIFY) Fix &readpoly() and implement &read4x4() Modify 3dNwarpApply to use same function as &apply() so that the 2 programs are in sync. Release 3dNwarpCalc into the wild: Born free, and code is worth running, but only worth running, because you're born freeware! 19 Aug 2011, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY) added the ability to output 1D sresp datasets Requested by S Baum.
18 Aug 2011, RW Cox, 3dttest++, level 1 (MICRO), type 0 (GENERAL) Add some clarify text about covariates to the -help output Also add an addition check to see if dataset name covariates are all the same, and print out some info about the covariates. 18 Aug 2011, RW Cox, 3dNwarpCalc, level 1 (MICRO), type 0 (GENERAL) Add '&apply' function To apply a calculated 3D warp to a dataset, without having to use 3dNwarpApply
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.
12 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY) gave volreg 3dAllineate command priority for final anat
11 Aug 2011, RW Cox, 3dNwarpCalc, level 1 (MICRO), type 0 (GENERAL) Added sqrt of a nonlinear warp to the repertoire.
09 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 1 (NEW_PROG) Implemented about 80% of it Seems to work, but needs a fair amount of fine tuning and testing. 09 Aug 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add '-cvarinv' option for Vinai
04 Aug 2011, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY) wrote loc_strcpy(/cat)_realloc for MCW_file_expand This is to allow for long sub-brick selectors.
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. 03 Aug 2011, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 2 (NEW_OPT) added -save_orig_skullstrip, to avoid oblique transforms This was added for afni_proc.py.
02 Aug 2011, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT) Add '-inmask' option, to use internal mask To be compatible with AFNI's Clusterize GUI, which was also modified to output this option when appropriate. 02 Aug 2011, RC Reynolds, uber_skel.py, level 1 (MICRO), type 5 (MODIFY) main class inherits object - for older versions of python 02 Aug 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY) main class inherits object - for older versions of python 02 Aug 2011, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY) added control var out_prefix, a prefix for output files
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) 01 Aug 2011, ZS Saad, Draw Dataset, level 2 (MINOR), type 5 (MODIFY) Changed the gap selection to arrows to allow for much larger gaps 01 Aug 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Clusterize minor changes * Shift+3clust button = actually run the 3dclust command, in addition printing it out * Add a warning message if an internal 3dClustSim mask is present, since 3dclust results will vary from Clusterize * Add Jumpto buttons to AFNI crosshair label popup menu
29 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE) z.max files are now named by p-value And suggest a quick.alpha.vals.py command. 29 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 5 (MODIFY) changes to handle python 2.4, where shell output has extra blank lines 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.
26 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) if e2a, update current anat to skull-stripped anat from align block This would avoid a second skull-strip step in @auto_tlrc.
25 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE) added keepblocks var, to limit kept intermediate datasets
22 Jul 2011, ZS Saad, afni, level 1 (MICRO), type 3 (NEW_ENV) Added AFNI_TIME_LOCK to turn on AFNI's Time Lock by default 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, RW Cox, 3dttest++, level 1 (MICRO), type 5 (MODIFY) Add column selection to -covariates for this, also 21 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) changed TR counts to come via awk instead of grep 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, ZS Saad, 1dcat, level 1 (MICRO), type 2 (NEW_OPT) added -sel option to 1dcat with -sel one can apply the same selection of columns and rows to all files on the command line, allowing the use of wildcards when specifying input 1D files. 20 Jul 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 5 (MODIFY) Allow sub-brick selectors on the -covariates table 20 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 1 (NEW_PROG) program will generate a script to produce a p-value/q-value curve pair 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
15 Jul 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT) Add -center option for covariates (cf. Chen Gang) 15 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) save output from ss_review in out.ss_review.$subj.txt 15 Jul 2011, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE) applied -d as -defaults
14 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) added 'max motion displacement' to basic script 14 Jul 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_max_displace, for maximum motion displacement 14 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 6 (ENHANCE) show date per iter block and add ./ to 3dcalc prefix
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. 13 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) run gen_ss_review_scripts.py and any resulting 'basic' review script 13 Jul 2011, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 2 (NEW_OPT) added -exit0 and babbled about possible artifact tests
11 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 3 (MAJOR), type 1 (NEW_PROG) for generating single subject review scripts To be run by the afni_proc.py proc script or directly by users. 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. 11 Jul 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV) AFNI_ATLAS_COLORS and default atlas in AFNI GUI Set atlas to use for Atlas colors, Go to atlas location, Draw Dataset and Renderer. Name of atlas can be set in environment and modified in the AFNI GUI environmentalism menu. Several other environmental variables regarding atlas usage can also be modified there too.
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. 08 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 5 (MODIFY) added -on_surface, which might not end up being so useful
06 Jul 2011, RC Reynolds, uber_align_test.py, level 1 (MICRO), type 5 (MODIFY) test use of SUBJ.set_var_with_defs 06 Jul 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) create anat_final dset, as one that is aligned with the stats Also, suggest use of uber_subject.py in the -ask_me dialog.
05 Jul 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) add -NOLINE to include clipping of points outside the box 05 Jul 2011, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) minor enhancements to 5 python files (prep for gen_ss_review_scripts.py)
01 Jul 2011, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL) Replace text-only AFNI Tips with HTML-based Allows incorporation of images and better formatting. Uses XmHTML widget set, whose source code is also added to AFNI.
30 Jun 2011, RC Reynolds, afni_proc.c, level 1 (MICRO), type 5 (MODIFY) renamed aligned anat output (from align_epi_anat.py) This should make it clear whether or not the output anat should be used
28 Jun 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 3 (NEW_ENV) Ability to skip the 'centering' done in AM2 regression By setting environment variable AFNI_3dDeconvolve_rawAM2 to YES, as in the command 3dDeconvolve -DAFNI_3dDeconvolve_rawAM2=YES ...
27 Jun 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Add README.afnigui and AFNI Tips button 27 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) added -dset_index0_list/-dset_index1_list options, etc. - ttest++ and MEMA commands now apply directories to datasets - changed Subject.atrs to be VarsObject instance, not dictionary 27 Jun 2011, RC Reynolds, thd_table.c, level 1 (MICRO), type 5 (MODIFY) output warning hint on single column covariate file 27 Jun 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY) changed decode_1D_ints to take imax param Affects 1d_tool.py, xmat_tool.py and any utilities using lib_afni1D.py. Also added restrict_by_index_lists(). 27 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV) AFNI_WHEREAMI_DEC_PLACES Set precision for whereami output Higher field data and animal atlases require higher precision. The default value used for focus point among template spaces is still 0 decimal places (closest mm), but animal data requires three decimal places. Value may range from 0 to 10.
24 Jun 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) added global option -pif which is used to flag certain commands. -pif PROCESS_ID_FLAG is used to flag a particular AFNI command so that you can identify from the shell that command's process id by grepping for PROCESS_ID_FLAG on the output of 'ps -a'. 24 Jun 2011, RC Reynolds, slow_surf_clustsim.py, level 3 (MAJOR), type 1 (NEW_PROG) a temporary program until we do this in C
23 Jun 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 5 (MODIFY) Ability to INIT-ialize InstaCorr from a plugout Details are in README.driver, under the INSTACORR command section. 23 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV) Desai MPM atlases New maximum probability map atlases derived from the Desai probability maps just introduced in distribution.
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. 20 Jun 2011, ZS Saad, 3drename, level 1 (MICRO), type 2 (NEW_OPT) added support for -overwrite 20 Jun 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added eta2 function (alongside '3ddot -doeta2')
17 Jun 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Button3 (right) click image viewer 'Disp' to raise AFNI controller 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, 3dSurfMask, level 3 (MAJOR), type 2 (NEW_OPT) Major improvements for mask creation and voxel distance computations Option -fill_method SLOW produces more accurate masks for voxels inside the closed surface. In addition, the program outputs a dataset with the shortest distance of each voxel to the surface. See examples under 3dSurfMask -help. 16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT) -flip_orientation allows for reversing triangle orientation. See new examples under SurfPatch -help 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, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) added -doeta2 via new THD_eta_squared_masked Added for Shinchan. 16 Jun 2011, RC Reynolds, 3dAutoTcorrelate, level 1 (MICRO), type 4 (BUG_FIX) allowed very small datasets
15 Jun 2011, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT) Add -sum option; rearrange -help output a little. 15 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE) if constant dset names, extract SIDs from dir names Done for R Momenan.
10 Jun 2011, DR Glen, whereami, level 4 (SUPER), type 0 (GENERAL) Generic Atlas Support and new atlases Atlases, spaces and transformations are now defined in a NIML file, AFNI_atlas_spaces.niml. Transformations among spaces for coordinates are defined in that file for use by whereami and the whereami display in the AFNI GUI. The flexible naming of the spaces and atlases allows easy addition of new atlases to AFNI processing. Two new environment variables control what atlases and spaces are shown when no atlas is specified, AFNI_ATLAS_LIST and AFNI_TEMPLATE_SPACE_LIST The list of atlases now defaults to the TT_Daemon and the Eickhoff- Zilles atlases in MNI_ANAT space. Additionally, the cytoarchitectonic atlases from the Zilles, Eickhoff group have been updated to the most recent version, 1.8. ***The previous versions, 1.5, are not used in this release by default. Depending upon differences on how regions or codes are defined and used, it is possible that processing scripts and results may be affected. With this release, we also introduce three probabilistic atlases donated by the Desai group generated from a typical AFNI pipeline. These atlases contain a multitude of regions created using both @auto_tlrc and FreeSurfer.
08 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT) Added -npb and modified title bar to reflect bloc of ports You can have multiple instances of programs talking to each other. See afni's help for details on the -npb option. 08 Jun 2011, ZS Saad, @FSlabel2dset, level 2 (MINOR), type 1 (NEW_PROG) Script to change FreeSurfer ascii label file to SUMA dset 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
07 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT) Allow multiple instances of communicating programs per machine. This was done by generalizing option -np PORT_OFFSET which allows users to use a different set of ports for different AFNI/SUMA/etc. sessions.Port numbers should no longer be hard coded anywhere. New dedicat ed ports should be added to then new init_ports_list() function. 07 Jun 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added 'w' key for writing out colormap to disk. See suma's help for the colormap. (press ctrl+h with cursor over the colormap in the surface controller) 07 Jun 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) -np, -list_ports, -port_number* control and report port assignments See suma -help for details. 07 Jun 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) -list_ports, -port_number* give port assignment information See afni -help for details. 07 Jun 2011, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL) modify number of points used for optimization Powell's NEWUOA algorithm requires specifying number of points kept at each stage for approximating the objective function. Modification here is to change this number as the various steps of registration happen, using fewer points at the start and more at the final steps. Speeds things up a little.
06 Jun 2011, RW Cox, powell_newuoa.c, level 1 (MICRO), type 0 (GENERAL) Remove 'static' and initialize all variables to 0. Makes tiny differences in 3dAllineate results. Hmmm.
03 Jun 2011, RC Reynolds, Makefile, level 2 (MINOR), type 2 (NEW_OPT) removed -lpng from Makefile.macosx_10.6_Intel_64 We added -lpng because we were compiling our own OpenMotif (configure option?), but fink's version does not need it. 03 Jun 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -volreg_compute_tsnr/-regress_compute_tsnr Volreg TSNR is no longer the default, but regress TSNR is.
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) compute TSNR datasets (added -compute_tsnr); added -regress_make_cbucket 02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) de-meaned motion regressors is now the default - added -regress_apply_mot_types to specify motion types for regression - added -regress_no_motion_demean and -regress_no_motion_deriv - by default, demean and deriv motion parameters are created - by default, demean motion parameters are applied in the regression (replacing the original 'basic' parameters, which should have no change in betas of interest, just the constant polort betas)
31 May 2011, RW Cox, data loading, level 1 (MICRO), type 0 (GENERAL) Allow mmap for supra-2GB .BRIK files Change DBLK_mmapfix macro (3ddata.h) to work for larger files on 64-bit systems -- with sizeof(size_t) == 8. Also print an informative message in thd_loaddblk.c when mmap-ing more than 1GB.
27 May 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) re-work of motion, as prep for more motion options - replaced -volreg_regress_per_run with -regress_motion_per_run - made uniq_list_as_dsets() a warning, not an error (for J Britton) 27 May 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -split_into_pad_runs (for regress motion per run)
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. 26 May 2011, RW Cox, mri_read, level 1 (MICRO), type 5 (MODIFY) Add warning message for ANALYZE scale factors too big or too small 26 May 2011, RW Cox, All, level 1 (MICRO), type 0 (GENERAL) new AFNI version as of today Just because -- it's been 7 months.
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 25 May 2011, RW Cox, @1dDiffMag, level 1 (MICRO), type 1 (NEW_PROG) Computes magnitude of 1st differences of 1D file 25 May 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add -tdiff option == statistics on first differences of data 25 May 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -global_to_local and -local_to_global for G Chen
24 May 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add -noline and -box options To plot markers at each point, without or with lines connecting them. 24 May 2011, RC Reynolds, 1dplot, level 2 (MINOR), type 4 (BUG_FIX) fixed plotting of varying length time series
20 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 2 (NEW_OPT) Add normal theory CI for Pearson; Add -block option Pearson correlation (the default) now gets the normal theory confidence interval printed at no extra charge. To allow for serial correlation, the -block option enables random length block resampling bootstrap. Add some more help text to explicate things a little better. 20 May 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY) execute via /usr/bin/env python Help now suggests fink as primary Mac source for PyQt4. 20 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 5 (MODIFY) execute via /usr/bin/env python
19 May 2011, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added support for multiple reference time series. Search for -var* options in @RetinoProc -help. 19 May 2011, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 2 (NEW_OPT) Added option to use best of multiple reference time series. Search for -multi_ref_ts in 3dRetinoPhase -help 19 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 1 (NEW_PROG) Compute correlation coefficients of 1D columns Pearson, Spearman, Quadrant, or Kendall tau_b. Main goal is to provide the bias-corrected bootstrap estimate of the 95% confidence interval.
18 May 2011, ZS Saad, @RetinoProc, level 3 (MAJOR), type 2 (NEW_OPT) Added options for mapping to specific layers, and the use of delay The options -wm, -pial, etc. allow for tight control of mapping onto specific layers in the cortex. Option -delay improves latency estimation compare to using the phase of the fundamental frequency. 18 May 2011, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 2 (NEW_OPT) Added options to 3dRetinoPhase to estimate latency as in 3ddelay The two options for computing delays, instead of phase, are -phase_estimate DELAY, and -ref_ts REF_TS . See program's -help for details. Also added -ort_adjust which is needed to account for lost DOF in external detrending when estimating the significance of correlation coefficients with delay estimation. The program now output a correlation coefficient with the visual field angles datasets. And speaking of correlation coefficients, the significance levels should be taken with a grain of salt, especially in derived datasets such as field angle, and VFR in SurfRetinoMap. 18 May 2011, ZS Saad, SurfRetinoMap, level 2 (MINOR), type 5 (MODIFY) Added a correlation coefficient with VFR output. 18 May 2011, ZS Saad, 3ddelay, level 2 (MINOR), type 2 (NEW_OPT) Added options to 3ddelay to improve its utility for retinotopy analysis The new options are -phzreverse and -phzscale. Though useful, you are better off using 3dRetinoPhase -phase_estimate DELAY option. It is much more convenient for retinotopy analysis and fits better in @RetinoProc 18 May 2011, ZS Saad, suma, level 1 (MICRO), type 4 (BUG_FIX) Node value now updates when switching dsets while viewing surf patches.
16 May 2011, RW Cox, afni, level 1 (MICRO), type 5 (MODIFY) Make 'Points' display in grapher get bigger with thicker lines Otherwise, thick lines hide the points. Done via XFillArc function. 16 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE) could be used as a release version - added 'check center dist' button, to display the current distance - added menu item to show afni command for viewing results - added menu items to show python and shell command windows - added much more help, including main and section buttons - added browsing of align_epi_anat.py help 16 May 2011, RC Reynolds, afni_util.py, level 1 (MICRO), type 6 (ENHANCE) added exec_tcsh_command function 16 May 2011, RC Reynolds, @Center_Distance, level 1 (MICRO), type 6 (ENHANCE) return something to $status, so we can detect success or failure
13 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE) added working GUI (for options, GUI help still needs ... help)
12 May 2011, RC Reynolds, uber_skel.py, level 3 (MAJOR), type 1 (NEW_PROG) A working skeleton for future uber programs. This is based on uber_align_test.py, version 0.2. 12 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE) many small updates This set of 3 files was broken off set uber_skel.py, meant to be a resonable starting point for future uber programs.

auto-generated by afni_history on May 10 2013