AFNI HISTORY

level 2 and higher

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


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

---- log of AFNI updates (most recent first) ---- 30 Jul 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) copy tlrc_base/template to results dir; add opt -tlrc_copy_base Done for QC and visualization purposes; requested by P Taylor.
29 Jul 2022, RC Reynolds, afni_base.py, level 2 (MINOR), type 5 (MODIFY) update locate() : return 1 if found, even via @Find
28 Jul 2022, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) add -Wl,-headerpad_max_install_names to linker command Make space for install_name_tool -change to use @executable_path. Thanks to witherscp on MB for noting the problem.
26 Jul 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) when warping an anat follower, if appropriate, copy the label table Done at the behest of the mighty P Taylor.
04 Jul 2022, P Taylor, 3dLocalUnifize, level 2 (MINOR), type 2 (NEW_OPT) Well, a new arg for '-local_mask ..' opt. Use arg value 'None' to turn off the default automasking now.
17 Jun 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 2 (NEW_OPT) add and apply nifti_image_write_status in NIFTI-1 and -2
06 Jun 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -align_unifize_epi local method, -align_opts_eunif To apply 3dLocalUnifize from P Taylor. 06 Jun 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Add new ve2a QC, via new uvar final_epi_unif_dset. Also scale ulay=EPI brightness better for EPI-to-anat align imgs.' 06 Jun 2022, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Some new opts to control ulay brightness, esp. for APQC HTML. New opts: '-ulay_range_am ..' and '-ulay_min_fac ..' 06 Jun 2022, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Some new opts to control ulay brightness, esp. for APQC HTML. New opts: '-ulay_range_am ..' and '-ulay_min_fac ..'
03 Jun 2022, P Taylor, 3dLocalUnifize, level 2 (MINOR), type 1 (NEW_PROG) New program for unifizing brightness. Should be helpful for alignment.
24 May 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add option -command_comment_style As requested by the ominous P Taylor.
17 May 2022, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 2 (NEW_OPT) add to prog lists
11 May 2022, P Taylor, SurfLocalstat, level 2 (MINOR), type 4 (BUG_FIX) The 'mean' stat was accumulating int, not float, values. This effective truncation/'digitizing' error should be fixed now.
10 May 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) do not add global line wrapper to QC block Avoid line wrappers in the generation of out.ap_uvars.txt (might happen when copy_anat dset has a very long name, for example). Thanks to E Chang for pointing out the issue.
06 May 2022, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) add functions slice_pattern_to_order, slice_pattern_to_timing
03 May 2022, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) for anyos_* packages, test for update using AFNI_version.txt
02 May 2022, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add distribution packages anyos_text and anyos_text_atlas
29 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) prepare for the all-important anyos_text distribution Add Makefile.anyos_text and an install_text target in Makefile.Include. 29 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) apply PRId64 for some int64_t printing Modified niml.h, niml_elemio.c, mri_transpose.c, thd_loaddblk.c.
28 Apr 2022, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX) afni_util.py:common_dir() : watch for the deadly JR scenario! Thanks to J Ritchie for unconvering this, peculiar, issue.
27 Apr 2022, RC Reynolds, Makefile.macos_11_ARM_clang, level 2 (MINOR), type 5 (MODIFY) (w/dglen) modify recent mac builds to get all X packages from homebrew Modified Makefile.macos_11_ARM_clang, Makefile.macos_10.15_clang, and the corresponding other_builds/OS_notes files.
23 Apr 2022, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT) Can specify which shell to use, because there are newer shell(s). That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 23 Apr 2022, P Taylor, @afni_refacer_make_master_addendum, level 2 (MINOR), type 0 (GENERAL) Now creates a v2.0 of the shell. The new shell removes more face. Asked for by A. Basavaraj.
22 Apr 2022, RC Reynolds, Dimon, level 3 (MAJOR), type 2 (NEW_OPT) add -sort_method cases rin and geme_rin 22 Apr 2022, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT) add -no_frivolities option, to directly set that 22 Apr 2022, P Taylor, afni, level 2 (MINOR), type 4 (BUG_FIX) The '-bysub ..' opt wasn't working, because a 'find' cmd was bad. Reformatted the 'find', though it might still benefit from other tweaks.
14 Apr 2022, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 4 (BUG_FIX) Replacement was not occuring if ROIs were purged by modal smoothing. Fixed that bug, hopefully improving robustness to such error in future.
12 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) add Makefile.linux_fedora_35_shared and OS_notes.linux_fedora_35.txt
06 Apr 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) allow for REML-only errts on surface Thanks to P Molfese for bringing it up.
05 Apr 2022, RC Reynolds, 3dTshift, level 2 (MINOR), type 6 (ENHANCE) allow for shifting a single slice (or voxel) time series Also, add a help example demonstrating this.
01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT) Add '-disp_def_params' so the user can see the default params. The params will also now get displayed during runtime. 01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT) Add many more '-min_* ..' options for controlling badness criteria. Asked for by user nseider: hope these are helpful! 01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 5 (MODIFY) Actually output the number of bad slices per volume. Previously had some ~fancy encoding about criterion of badness (why?). 01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT) New opts '-dont_use_*' to turn off some of the drop criteria at will. Also put in help descriptions about drop criteria, in Notes.
22 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add ap_uvars dir_suma_spec, suma_specs Also, remove inappropriate -epi_strip from -align_opts_aea in example.
16 Mar 2022, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_tr_offsets See Example 10 d.
15 Mar 2022, RC Reynolds, afni_util.py, level 2 (MINOR), type 4 (BUG_FIX) cast run_time_to_polort output to int, for py2.7 Thanks to P Taylor for pointing it out.
12 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) use aea.py instead of allin for extra -align_epi_ext_dset registration align_epi_anat.py would deal with a difference in obliquity
10 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) run 3dAllineate for -align_epi_ext_dset to volreg base
09 Mar 2022, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX) Patch unfathomable problem with -permute and -covariates combined Covariate matrices are constructed BEFORE permutation is setup, and that caused a problem. Patched around that.
08 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) apply -polort in @radial_correlate
07 Mar 2022, RC Reynolds, @radial_correlate, level 2 (MINOR), type 2 (NEW_OPT) add -polort; default is 2
02 Mar 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with nifti_clib repo
01 Mar 2022, RC Reynolds, nifti_tool, level 3 (MAJOR), type 2 (NEW_OPT) allow conversion between any 2 int or float types (except float128) Add -copy_image, -convert2dtype, -convert_verify, -convert_fail_choice. Conversion operations happen in nt_image_read and nt_read_bricks, and can therefore be applied to most data-included operations. Requested by J Teves.
20 Feb 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with nifti_clib
18 Feb 2022, RC Reynolds, @Install_APMULTI_Demo2_realtime, level 3 (MAJOR), type 1 (NEW_PROG) new install script for APMULTI_Demo2_realtime This is a demo for running AFNI's real-time system, without needing to bother the scanner. It demonstrates use if single- and multi-echo DICOM input, and various sets of data that can be passed from afni to an external program (realtime_receiver.py in this case).
16 Feb 2022, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE) propagate obliquity in case of -ftype AFNI 16 Feb 2022, P Taylor, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT) Add opt '-compressor ..' so AFNI_COMPRESSOR env var can be set. Leads to created *.BRIK dsets getting compressed on disk.
14 Feb 2022, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_keepers Show table of subjects kept, rather than those with any outliers. Added on the authority of P Taylor.
12 Feb 2022, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT) 3dMean can compute max, min, absmax, signed_absmax 3dMean keeps only one dataset in memory at a time and can process thousands of datasets. These options emulate the options across time in 3dTstat
10 Feb 2022, RC Reynolds, afni_python_wrapper.py, level 2 (MINOR), type 4 (BUG_FIX) change import to try from afnipy first Biowulf has old afnipy/*.py files in abin. Thanks to P Kusmierek and P Taylor for reporting the problem.
09 Feb 2022, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fix FIR blur padding As noted by PT, volumes were not being properly blurred near edges. Fix edge padding to be applied for entire FIR length, not just at full FIR offset.
08 Feb 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -html_review_opts for passing options to apqc_make_tcsh.py Done for S Torrisi. 08 Feb 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 2 (NEW_OPT) AP now can pass some '-html_review_opts ..' values to this prog. First one: '-mot_grayplot_off', for envelope-pushing user S Torrisi.
07 Feb 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) create out.ap_uvars.json, and apply via gssrs -init_uvas_json A minor assist in helping P Taylor take over this spiral galaxy arm... 07 Feb 2022, P Taylor, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Add a new stat: MCONEX, the Michelson Contrast of Extrema. mconex = |A-B|/(|A|+|B|), where A=max and B=min.
06 Feb 2022, P Taylor, 3dedgedog, level 2 (MINOR), type 0 (GENERAL) If -only2D opt is used, then don't blur in 3D, either. Also turn off optimized double blurring---essentially not time diff. 06 Feb 2022, P Taylor, 3dedgedog, level 2 (MINOR), type 4 (BUG_FIX) Fix some badness when 4D datasets are input. Also have a better scale value, based on 3dLocalstat sigma.
03 Feb 2022, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT) add -init_uvas_json Allow passing a json file, akin to passing many -uvar options.
29 Jan 2022, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT) add -extras_on_one_line To display any 'extra' values using only one line, per TR.
27 Jan 2022, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add options -write_sep, -write_style, to control format of output
26 Jan 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Update QC block: vorig now shows the epi-anat overlap. Shows overlap with ignoring obliquity and applying it (if present). 26 Jan 2022, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 4 (BUG_FIX) Fix how -box_focus_slices opt works if one of the AMASK* keywords is used. Previously was producing error, not recognizing it wasn't a dset.
25 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Update QC block: vorig now shows the 'copy_anat' dset. Applies in all cases; AP just passes along uvar. Thanks, RCR! 25 Jan 2022, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 2 (NEW_OPT) Add in existin chauffeur options: -no_cor, -no_axi, -no_sag. For APQC---vorig of initial overlap.
24 Jan 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) pass combine_method to gen_ss_review_scripts.py This will be applied to the 'mecho' APQC section by P Taylor.
20 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Update QC block: vstat (for task-based FMRI cases). There will now be typically up to 5 stats dsets shown (GLT and other).
18 Jan 2022, RC Reynolds, @Install_APMULTI_Demo1_rest, level 3 (MAJOR), type 1 (NEW_PROG) (w/PT) new install script for APMULTI_Demo1_rest This is a demo for running various multi-echo processing methods on resting state data via afni_proc.py. (renamed from @Install_AP_MULTI_DEMO1) 18 Jan 2022, RC Reynolds, 3dDiff, level 2 (MINOR), type 5 (MODIFY) remove declarations after statements and init any free'd pointers 18 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Add a new QC block: mecho. This is for multi-echo (ME) FMRI; mostly for m_tedana right now. 18 Jan 2022, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL) New functions/functionality for the new QC block: mecho. Also tweaked/updated the help.
13 Jan 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Do a check if the user asks for 'pythonic' APQC. If their system CAN'T HANDLE THE TRUTH, then downgrade kindly to 'basic'.
12 Jan 2022, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL) got rid of remaining uninit warnings (even if code was okay) 12 Jan 2022, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 4 (BUG_FIX) Add '-save_ftype ..' opt to this script, to make @animal_warper happy. Thanks, DRG, for pointing this out. 12 Jan 2022, P Taylor, 3dDepthMap, level 2 (MINOR), type 0 (GENERAL) Rename program: 3dEulerDist -> 3dDepthMap. The original name was odd for *Euclidean* Distance Transform, anyways...
11 Jan 2022, RC Reynolds, tedana.py, level 2 (MINOR), type 5 (MODIFY) even without -seed, always apply a seed (default = 42) Now 2 executions should produce the same result, unless -seed is modified. This matches the MEICA group tedana. 11 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) add option -disp_ver_matplotlib Done under the now-even-more-strict-than-before orders from P Taylor. 11 Jan 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) rename -combine_method m_tedana_tedort to m_tedana_m_tedort Reserve the former for future tedort projection via AFNI. 11 Jan 2022, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) if missing, init .afnirc/.sumarc
10 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) matplotlib is required ; check version >= 2.2
05 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) check for having both .cshrc and .tcshrc
29 Dec 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -write_simple_tsv Also, read and write default mod_* modifier columns. 29 Dec 2021, P Taylor, 3dedgedog, level 2 (MINOR), type 0 (GENERAL) Change default sigma_rad to be 1.4, not 2.0, to capture more details. This is because results look much better in human T1w dset.
26 Dec 2021, P Taylor, 3dedgedog, level 2 (MINOR), type 2 (NEW_OPT) The -automask (and -automask+X) functionality is now, well, functional. The '-mask ..' option appears to be working, too. 26 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 0 (GENERAL) Give correct name of opt in prog help: -bounds_are_not_zero. Had forgotten the '_not' part previously. Whoops.
24 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 2 (NEW_OPT) Can process some dsets much faster now, with opt '-binary_only'. This is to flag that the input is a binary mask.
19 Dec 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) misc updates for circleCI build based on xcode 12.4.0 Remove thd_incorrelate.o from cmake libmri, etc. 19 Dec 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_distmat Display nrows x nrows matrix of distances between all vector row pairs. Option added for jkblujus (AFNI MB).
15 Dec 2021, RW Cox, prefiltered args, level 2 (MINOR), type 2 (NEW_OPT) Bulk input arguments These '< 09 Dec 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX) balls were not verified to be entirely within dset bounds Thanks to aclyn11 (AFNI MB) for noting the problem. 09 Dec 2021, RC Reynolds, 3dinfo, level 2 (MINOR), type 5 (MODIFY) further restrict -same_center Change def limit from 0.1*sum_vox_diags to 0.001*ave_vox_diag.
08 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 0 (GENERAL) Already change something internally about only2D calcs. Should just be simple change, being more general. 08 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 2 (NEW_OPT) Can run in 2D now, with opt '-only2D ..'. For Daniel Glen.
03 Dec 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add -combine_method m_tedana_tedort Now have MEICA group tedana methods: m_tedana, m_tedana_OC, m_tedana_tedort
01 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 4 (BUG_FIX) Was getting incorrect voxel scaling along a couple axes---fixed now. Also re-arrange functions to be easier to call from other funcs.
30 Nov 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 1 (NEW_PROG) New C prog for Eulerian Distance Transform (EDT) for ROI-based dsets. Calculate distances to boundaries within a FOV.
24 Nov 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX) make boxes tight; scale radius to voxel counts Tighten boxes and balls to not include unrequested voxels. Scaling the radius allows for sub-mm voxels.
21 Nov 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add updates for current tedana; add -help_tedana_files
15 Nov 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) pull THD_nifti_process_afni_ext() out of thd_niftiread.c:THD_open_nifti() This should have no effect. It is preparation for testing the AFNI extension in NIFTI against dset.
07 Nov 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -regress_opts_fwhmx (for adding options to 3dFWHMx) Added on the authority of S Torrisi.
29 Oct 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) on mac, check for standard R not in PATH 29 Oct 2021, P Taylor, @Install_NMT, level 2 (MINOR), type 0 (GENERAL) Update macaque template+atlas data. Now working/defaulting to NMT v2.1. 29 Oct 2021, P Taylor, @Install_MACAQUE_DEMO_REST, level 2 (MINOR), type 0 (GENERAL) Update macaque demo for resting state FMRI processing. New scripts, now working/defaulting to NMT v2.1.
27 Oct 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) try to warn on insufficient disk space Check if any data partition has less than 5 GB available. Done to appease the mighty P Taylor. 27 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX) Opt '-extra_qw_opts ..' had wrong name in help file, '-qw_opts ..'. Corrected this, as well as usage.
25 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Improve QC outputs, and fix some chauffeur ranges. Hopefully easier to evaluate alignment now, among other features.
23 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) For ROI image QC, use ROI_glasbey_2048 now by default. CHARM has ROI values >256, so might as well go all in.
21 Oct 2021, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) allow for previously set DYLD_LIBRARY_PATH
20 Oct 2021, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 6 (ENHANCE) do not allocate errts/fitts on -x1D_stop
08 Oct 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_xmat_stype_cols Display xmat columns for speicified -stim_* regressor classes.
02 Oct 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Copy input anat (and any mask_ss) into the output directory. Can be useful for checking if things went awry (do they ever?!?).
01 Oct 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_xmat_stim_info Display xmat info for -stim_* regressor classes.
29 Sep 2021, P Taylor, 3dAllineate, level 3 (MAJOR), type 0 (GENERAL) 3dAllineate: set -lpa+ to re-include 'ov' in its recipe---for stability. This makes it closer to historical form (but no 'mi' still). 29 Sep 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL) Just running '-help' leads to lesion_outs.txt to be created and populated. ... and it also got overwritten oddly. Move those lines further down. 29 Sep 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 4 (BUG_FIX) Fix behavior with longnames---just needed a quote around var. Should work now. Also update help.
27 Sep 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV) AFNI_INSTACORR_JUMP If YES (default), Shift+Ctrl+click sets the instacorr seed and jumps the crosshairs to that location. If NO, sets the instacorr seed but there is no crosshair jump. (For Phil Kohn) 27 Sep 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_imit2w_from_t1w, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_decmap, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_convert_dcm_anat, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @djunct_4d_imager, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @afni_refacer_run, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls. 27 Sep 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) On/about Aug 23, 2021, default label_sizes in image windows changed. That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
23 Sep 2021, P Taylor, @epi_b0_corr.py, level 2 (MINOR), type 2 (NEW_OPT) Had been missing the internal processing of option '-epi_pe_bwpp'. ... which has now been added in. 23 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can now perform clusterizing, with Alpha+Boxed on, like in GUI. New opt '-clusterize ..' for some commands; see help/NOTES for full info.
21 Sep 2021, RC Reynolds, 3dTshift, level 2 (MINOR), type 6 (ENHANCE) propagate toffset, if not zero 21 Sep 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 2 (NEW_OPT) Add in new opts to turn off images in particular view planes being made. These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC. 21 Sep 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 2 (NEW_OPT) Add in new opts to turn off images in particular view planes being made. These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC. 21 Sep 2021, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Add in new opts to turn off images in particular view planes being made. These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC. 21 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Add in new opts to turn off images in particular view planes being made. These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC.
20 Sep 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL) apsearchize. Make help visible in editor with '@grayplot -hview'. 20 Sep 2021, P Taylor, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT) Add '-raw_with_bounds ..' to display raw values in arbitrary interval. Maybe most useful if data have been scaled.
31 Aug 2021, RW Cox, 3dTcorr1D/3dTcorrelate, level 2 (MINOR), type 4 (BUG_FIX) Change labels and statcode for -Fisher option Sir Paul pointed out that these programs didn't have the correct statcode when the Fisher transform was ordered, and also that the labels were confusing. Fixed it so if -Fisher was used, the statcode is FIZT vs FICO, and the labels have 'atanh()' 31 Aug 2021, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add option -gert_chan_digits, to specify num digits for channel in name 31 Aug 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Change default cost function to 'lpa', from 'ls'. Should be better? There is an opt to change, as necessary.
30 Aug 2021, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) New opts: '-all_roi_zeros' and '-automask_off'. Basically, N ROIs can have NxN mat, even if ROI ave is all zeros.
20 Aug 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -write_tsv_cols_of_interest
17 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 6 (ENHANCE) Modified to use OpenMP 3dTfitter.c, thd_fitter.c, and thd_lasso.c
10 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 1 (NEW_PROG) Add -LCB option for block-wise LASSO penalties LCB = LASSO Centro Block The penalty in a block is sum{ ABS[ beta[i] - centromean(beta[i],...) ] } which is intendend to make all the beta[i] in a block shrink towards a common value, rather than towards 0. The intent is to use this with IM regression models from 3dDeconvolve, to reduce outliers in the stimulus-wise beta estimates. 10 Aug 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 5 (MODIFY) No longer worry about even/odd slice output (and remove '-no_fs_prep'). Dealt with an old non-issue.

auto-generated by afni_history on Aug 5 2022