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 1 

---- log of AFNI updates (most recent first) ---- 03 Aug 2022, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX) 3dDeconvolve currently misbehaves when there are no events for IM Have the program terminate with an error, until the problem is resolved. Thanks for T Clarkson for pointing out the problem.
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.
27 Jul 2022, P Taylor, dsetstat2p, level 1 (MICRO), type 0 (GENERAL) Expand output precision and scale of calculability. Program used to run into trouble for large stat (bc of bc); now better. 27 Jul 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX) In mecho block when using m_tedana on Mac OS: fix copying tedana QC HTML. Swap cp -> rsync, because Mac OS cp opts are diff than on Linux.'
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.
22 Jul 2022, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY) add linux_fedora_28_shared; we now distribute linux_fedora_35_shared
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.
24 Jun 2022, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 5 (MODIFY) apply mask_epi_anat in help examples, rather than full_mask
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
13 Jun 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) remove essentially duped final_epi_unif dset and uvar
07 Jun 2022, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 4 (BUG_FIX) Fix how the AMASK_FOCUS_* keywords apply for '-box_focus_slices ..'. They didn't work before, but now do/should/might/perhaps/pleeeez.
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.
18 May 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX) allow for pb00 dsets in standard space Thanks to Erik (MB audachang) for noting it.
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. 10 May 2022, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 2 (NEW_OPT) Add -echo opt, and can propagate. For debugging 10 May 2022, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 2 (NEW_OPT) Add -echo opt, and can propagate. For debugging 10 May 2022, P Taylor, @SSwarper, level 1 (MICRO), type 2 (NEW_OPT) Add -echo opt, and can propagate. For debugging 10 May 2022, P Taylor, @SSwarper, level 1 (MICRO), type 0 (GENERAL) Update/fix to mask resampling if present and if deobliqueing with 3dWarp. Replace wsinc5 interp with NN interp---better for mask. Thanks, RCR!
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 03 May 2022, RC Reynolds, uber_subject.py, level 1 (MICRO), type 0 (GENERAL) update to deal with minor changes to python modules
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.
04 Apr 2022, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY) update .circleci/config.yml, using docker version 19.03.13 to 20.10.11 Done with P Taylor.
01 Apr 2022, RC Reynolds, @radial_correlate, level 1 (MICRO), type 4 (BUG_FIX) create ulay in all cases 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.
20 Mar 2022, P Taylor, apqc_make_html.py, level 1 (MICRO), type 4 (BUG_FIX) Fix display of subj ID from 'Top' button in case when subj ID starts num. In such cases, the unicode char for next line was misinterpreted.
18 Mar 2022, RC Reynolds, eg_main_chrono.py, level 1 (MICRO), type 6 (ENHANCE) add a little more edu
17 Mar 2022, RC Reynolds, @radial_correlate, level 1 (MICRO), type 5 (MODIFY) change saved ulay to be from orig EPI (to avoid detrended one) Done to appease the scrutinous P Taylor.
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 10 Mar 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX) Fix bug in 'mecho' QC block when m_tedana used with multiple runs. All buttons used to point to r01; now fixed.
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
06 Mar 2022, RC Reynolds, @diff.tree, level 1 (MICRO), type 2 (NEW_OPT) add -diff_prog
03 Mar 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) update block help; rename to quality control review
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. 01 Mar 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) fix removal of spaces with -combine_opts_tedana Thanks to J Teves for noting the problem. 01 Mar 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) make pythonic the default html_review_style Done to appease the ever-demanding P Taylor.
28 Feb 2022, RC Reynolds, 3dZcutup, level 1 (MICRO), type 4 (BUG_FIX) fix typo in bounds check on -keep (was backward) Thanks to Yixiang (on AFNI MB) for letting us know.
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.
15 Feb 2022, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 5 (MODIFY) display SHOW_KEEP for subjects on -show_keepers
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. 10 Feb 2022, RC Reynolds, 3dPval, level 1 (MICRO), type 4 (BUG_FIX) fix dealing with an unknown option Previously warned, but forgot to skip option (or break, depending). Change to failure. 10 Feb 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX) The 'pythonic' should be run if matplotlib ver is >=2.2, not just >2.2. Used incorrect comparison operator earlier. I know bc Biowulf told me so.
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. 03 Feb 2022, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) add data_file_to_json() This is a file conversion function that uses the util library. 03 Feb 2022, P Taylor, @chauffeur_afni, level 1 (MICRO), type 2 (NEW_OPT) Two new opts, using existing AFNI env vars Now have '-left_is_left ..' and '-left_is_posterior ..'.
01 Feb 2022, P Taylor, @SSwarper, level 1 (MICRO), type 0 (GENERAL) Some clearer error messaging (esp. if not '-base ..' is used). Remove any non-programmatic exclamation marks--even from comments.
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. 29 Jan 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) do not apply -execute if no new main script So -write_3dD_script will not -execute. 29 Jan 2022, RC Reynolds, README.environment, level 1 (MICRO), type 6 (ENHANCE) update AFNI_REALTIME_Mask_Vals with new modes Describe All_Data_light and ROIs_and_data.
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. 26 Jan 2022, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 4 (BUG_FIX) Fix how -box_focus_slices opt works in another aspect. Now should actually be used (had to turn off internal coord selection).
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. 24 Jan 2022, RC Reynolds, suma, level 1 (MICRO), type 4 (BUG_FIX) fix dupe symbol (clippingPlaneFile) error for mac 12 As reported by the international man of mistery, P Kundu. 24 Jan 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 2 (NEW_OPT) add combine_method uvar, to pass on to APQC 24 Jan 2022, P Taylor, 3dDepthMap, level 1 (MICRO), type 0 (GENERAL) Renaming some internal funcs, for clarity. Multi-ROI funcs get '_GEN' in name now, to distinguish from '_BIN' ones.
22 Jan 2022, P Taylor, 3dDepthMap, level 1 (MICRO), type 0 (GENERAL) Add functionality to '-rimify RIM' opt. A negative RIM value now leads to creating an anti-rim (or core) ROI. 22 Jan 2022, P Taylor, 3dDepthMap, level 1 (MICRO), type 2 (NEW_OPT) Add in the '-rimify RIM' opt, where RIM is a numerical value. Transform ROIs into boundaries up to depth RIM.
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).
19 Jan 2022, RC Reynolds, plug_realtime, level 1 (MICRO), type 6 (ENHANCE) slight addition to help and verb output for External_Datatset mode
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 10 Jan 2022, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE) if no .tcshrc, create one to source .cshrc Done under strict orders from P Taylor.
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.
28 Dec 2021, RC Reynolds, 3dBrickStat, level 1 (MICRO), type 5 (MODIFY) commit pull request and further clarify -nan help Thanks to L Anderson for the pull request.
27 Dec 2021, P Taylor, balloon, level 1 (MICRO), type 0 (GENERAL) Use printf(...) to display the program help, not fprintf(stderr, ...). In this way, the Sphinx help docs can see it.
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. 26 Dec 2021, P Taylor, 3dedgedog, level 1 (MICRO), type 0 (GENERAL) Full histories in each output dset now. Had not been passing argc and argv previously.
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. 24 Dec 2021, P Taylor, 3dedgedog, level 1 (MICRO), type 0 (GENERAL) Because 3dEulerDist has new '-binary_only' opt, this prog is faster. This is because edgedog at the moment runs EDT on a binary dset.
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. 09 Dec 2021, P Taylor, 3dedgedog, level 1 (MICRO), type 2 (NEW_OPT) Add in '-only2D ..' opt, similar to 3dEulerDist's one. Now can get planar edges, instead of always volumetric ones. 09 Dec 2021, P Taylor, 3dEulerDist, level 1 (MICRO), type 4 (BUG_FIX) Fix new -only2D opt slice selection. Was not always getting correct planar direction; should be now.
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.
07 Dec 2021, P Taylor, 3dedgedog, level 1 (MICRO), type 2 (NEW_OPT) Add in optional scaling of edges, via '-edge_bnd_scale'. B Related but slightly different scaling based on '-edge_bnd_side' opt.
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 03 Dec 2021, P Taylor, 3dedgedog, level 1 (MICRO), type 1 (NEW_PROG) Calculate edges with the Difference of Gaussian (DOG) approach. Thanks to DR Glen and C Rorden for discussions/suggestions on this.
02 Dec 2021, P Taylor, afni, level 1 (MICRO), type 0 (GENERAL) Adding the description of existing option(s) in the program help. The opts are the synonyms: '-notcsv', '-notsv', '-nocsv'.
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. 30 Nov 2021, P Taylor, 3dEdu_01_scale, level 1 (MICRO), type 0 (GENERAL) Added many more internal comments, e.g., codebase references. Thanks for the discussion+suggestions, J Teves!
26 Nov 2021, RC Reynolds, 3dGrayplot, level 1 (MICRO), type 4 (BUG_FIX) cs_pv.c: xt no longer malloc'd 26 Nov 2021, P Taylor, 3dEdu_01_scale, level 1 (MICRO), type 0 (GENERAL) Renaming of 3dEduProg. Simplifying some inner workings Basic AFNI program example. 26 Nov 2021, P Taylor, 3dEduProg, level 1 (MICRO), type 1 (NEW_PROG) A new program for people to learn to write AFNI progs. Perhaps a bit more basic I/O and usage than 3dToyProg.
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. 24 Nov 2021, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY) put space_to_NIFTI_code() into libmri To satisfy the evil designs of afni_proc.py.
21 Nov 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add updates for current tedana; add -help_tedana_files
17 Nov 2021, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX) handle uninit and if block in debugtrace.c, suma_datasets.c
16 Nov 2021, P Taylor, afni_system_check.py, level 1 (MICRO), type 0 (GENERAL) Add 'SLURM cluster'-specific check for number of CPUs. Phase two of secret plan to steal all of Rick's programs. Bwahahahaha.
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.
13 Nov 2021, P Taylor, afni_system_check.py, level 1 (MICRO), type 2 (NEW_OPT) New '-disp_num_cpu' opt to display number of available CPUs. Phase one of secret plan to steal all of Rick's programs. Bwahahaha.
08 Nov 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) add -milestones, to show interesting milestones for the program 08 Nov 2021, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) add -milestones
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.
28 Oct 2021, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 5 (MODIFY) remove 2-run polort 0 cormat IDENTICAL automatic warnings Done for P Taylor, as they were getting flagged in APQC.
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.
22 Oct 2021, P Taylor, apqc_make_html.py, level 1 (MICRO), type 0 (GENERAL) Report a better output path in the 'done' message. The originally-output relative path was often not useful.
21 Oct 2021, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) allow for previously set DYLD_LIBRARY_PATH 21 Oct 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Max blowup factor is actually 8, not 4. So, allow that fuller range in the internal number check.
20 Oct 2021, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 6 (ENHANCE) do not allocate errts/fitts on -x1D_stop
18 Oct 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) allow user-defined ROIs/masks to be used with -mask_apply Thank to D Picchioni for the suggestion.
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, RC Reynolds, 3dTshift, level 1 (MICRO), type 6 (ENHANCE) update help to connect tzero to stimulus timing in 3dDeconvolve Might want to subtract 'tzero' from stimulus event times. 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.
10 Sep 2021, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 6 (ENHANCE) add web formatting to help
09 Sep 2021, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @djunct_glue_imgs_vert, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @djunct_anonymize, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @RenamePanga, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @Purify_1D, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @FindAfniDsetPath, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system. 09 Sep 2021, P Taylor, @4Daverage, level 1 (MICRO), type 0 (GENERAL) Shebang changed from csh to tcsh. For uniformity/simplicity, and to avoid issues on occasional system.
31 Aug 2021, RW Cox, 3dTcorr1D/3dTcorrelate, level 2 (MINOR), type 4 (BUG_FIX) Change labels and statcode for -Fisher option Sir Paul pointed out that these programs didn't have the correct statcode when the Fisher transform was ordered, and also that the labels were confusing. Fixed it so if -Fisher was used, the statcode is FIZT vs FICO, and the labels have 'atanh()' 31 Aug 2021, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add option -gert_chan_digits, to specify num digits for channel in name 31 Aug 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Change default cost function to 'lpa', from 'ls'. Should be better? There is an opt to change, as necessary.
30 Aug 2021, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) New opts: '-all_roi_zeros' and '-automask_off'. Basically, N ROIs can have NxN mat, even if ROI ave is all zeros.
22 Aug 2021, P Taylor, lib_afni1D.py, level 1 (MICRO), type 4 (BUG_FIX) Afni1D.uncensor_from_vector() had a syntax error in one print call'). Was missing a %, now fixed.
20 Aug 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -write_tsv_cols_of_interest
19 Aug 2021, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Change top-of-image drawn label to resize font if drawn too large
17 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 6 (ENHANCE) Modified to use OpenMP 3dTfitter.c, thd_fitter.c, and thd_lasso.c
14 Aug 2021, RC Reynolds, coxplot, level 1 (MICRO), type 4 (BUG_FIX) remove duplicate symbols zzzplt_ and zzpltr_ Done at the behest of D Glen.
10 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 1 (NEW_PROG) Add -LCB option for block-wise LASSO penalties LCB = LASSO Centro Block The penalty in a block is sum{ ABS[ beta[i] - centromean(beta[i],...) ] } which is intendend to make all the beta[i] in a block shrink towards a common value, rather than towards 0. The intent is to use this with IM regression models from 3dDeconvolve, to reduce outliers in the stimulus-wise beta estimates. 10 Aug 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 5 (MODIFY) No longer worry about even/odd slice output (and remove '-no_fs_prep'). Dealt with an old non-issue.

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