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_months 6 

---- 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 ..'.

auto-generated by afni_history on Aug 5 2022