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) ---- 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.
29 Jul 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 2 (NEW_OPT) Add in @chauffeur_afni functionality: -edgy_ulay.
27 Jul 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fix typo in cubic resampling for viewer/3dresample (afni_slice.c) Done with P Taylor. 27 Jul 2021, P Taylor, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fix typo in cubic resampling for viewer/3dresample (afni_slice.c) Copying Rick's fix. Thanks to user 'ymao' for raising this issue on the MB .
26 Jul 2021, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add options -dcx, -dcy, -dcz, dc3 This provides the center of the volumetric grid, in DICOM coords.
22 Jul 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -multi_durations_from_offsets Added on the authority of W-L Tseng.
20 Jul 2021, RW Cox, NIML library, level 3 (MAJOR), type 4 (BUG_FIX) NIML file: input failed if file over 2BG in size Due to storing filesize in int/long. Fix was to make it stored in int64_t, and fixing a few other places.
16 Jul 2021, RW Cox, AFNI driver and GUI, level 1 (MICRO), type 4 (BUG_FIX) Fix bug in overlay_label='xxx' driver Someone put the terminating NUL byte in wrong place. (Whoever did that should be beaten.) Also added the '\newline' escape as a way to add a line break to the overlay label string from the driver -- since control characters aren't really allowed. 16 Jul 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) unindent EOF command terminator in example Thanks to I Berteletti for noting the problem.
15 Jul 2021, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Change image overlay label plotting to allow for multiline strings Per DRG: multiline strings, being centered along the y-axis about their point of origin, would be pushed off the top of the image. Fixed by setting the y-coord of the origin point to include a factor for the number of lines. 15 Jul 2021, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT) add -empty_is_outlier, to treat empty fields as outliers The default reporting of blank outlier test vals is now as non-outliers. Use this option to report as outliers. Added for the mighty P Taylor.
13 Jul 2021, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 4 (BUG_FIX) fix '-separator whitespace' in the case of blank lines Thanks to P Taylor for noting the problem.
12 Jul 2021, RW Cox, Clusterize, level 1 (MICRO), type 6 (ENHANCE) Make min cluster size = 1 (from 2) for DR Glen.
09 Jul 2021, P Taylor, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT) New: '-aff_move_opt ..' to use more than just giant_move in aff step. Also bug fix for when no followers were entered.
30 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Tweak column names *again*. Add in extra check that 3D vols are specified (e.g., with selectors).
29 Jun 2021, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT) -log2 and -log10 options To convert statistics to minus the logarithm of p-value.
28 Jun 2021, RW Cox, NIML, level 2 (MINOR), type 4 (BUG_FIX) Change byte count output for NI_write_element to int64_t And a few other functions as well. Reason: someone tried to create a 2.8 GB .niml.dset file, which caused a problem when counting up the bytes output using a 32 bit int. Users -- what can you do with them? 28 Jun 2021, RW Cox, afni GUI, level 1 (MICRO), type 6 (ENHANCE) Add Linear back to Alpha fading, as well as default Quadratic Drive-able. Menu item under 'Thr' popup. 28 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Reformat report*.1D tables a bit: match key and col names. Also, improve/simplify/clarify names of cols. Thanks, Adam Messinger. 28 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Well, OK, not *really* a new opt---new values accepted for existing opt. The '-olay_alpha ..' can now take Linear or Quadratic (grazie, Bob).
25 Jun 2021, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) add -rand_post_elist_partition This will partition an already defined stim class into new ones. Added on the authority of S Haller.
24 Jun 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 0 (GENERAL) Add tracking thru optimization of original points That is, with -verb, print out the original index [o=X] as the stages of optimization proceed. This helps determine if the larger number of initial coarse trial candidates parameter sets actually produces viable contenders for the championship. 24 Jun 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 0 (GENERAL) Silence 3drefit warns if changing space of dsets (might confuse users). Unnecessary warning for these temp dsets within the script.
23 Jun 2021, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY) Add the setjmp/longjmp escape mechanism to plusminus warping To gracefully end the program if the OpenMP race condition arises.
22 Jun 2021, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX) calm those grumpy compilers Issues noted by P Taylor. 22 Jun 2021, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY) without -datum, the output now depends on the map func, not the BRIK Done to appease the mysterious D Glen. 22 Jun 2021, P Taylor, SurfLayers, level 2 (MINOR), type 0 (GENERAL) Capture verbose output from ConvertSurface. Also add -no_clean opt. 22 Jun 2021, P Taylor, 3dNwarpCalc, level 2 (MINOR), type 0 (GENERAL) Put in std includes to be able to build on Mac with Clang. Though this program isn't even built...
21 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 5 (MODIFY) Change default blok type and radius for the lpc/lpa methods Old default was -blok 'RHDD(6.54321)'. New default is -blok 'TOHD(0)' where the 0 radius means to compute the blok radius so as to give the blok a volume of 555 times the volume of a base dataset voxel. For 1x1x1 voxels, such as the MNI template, this results in 'TOHD(5.18)'. If users want the old setup, they'll have to use the old blok definition explicitly.
18 Jun 2021, P Taylor, @Install_SURFLAYERS_DEMO1, level 2 (MINOR), type 0 (GENERAL) Created by Sam Torrisi. Help added, temp placeholder data now in place. Will add full demo data soon... 18 Jun 2021, P Taylor, @Install_AP_MULTI_DEMO1, level 2 (MINOR), type 0 (GENERAL) Adding install script for afni_proc.py multi-echo FMRI demo (OHBM, 2021). Demo authors: RC Reynolds, SJ Gotts, AW Gilmore, DR Glen, PA Taylor.
15 Jun 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_imit2w_from_t1w, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_decmap, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_convert_dcm_anat, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, ap_run_simple_rest.tcsh, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @toMNI_Awarp, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @simulate_motion, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 4 (BUG_FIX) Minor bug fix (never hit?), and avoid single line 'if' conds. Latter to avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @parse_name, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @parse_afni_name, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @move.to.series.dirs, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_in2out, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_erosion_thick, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @measure_bb_thick, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @global_parse, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @djunct_slice_space, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @djunct_glue_imgs_vert, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @compute_gcor, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @clip_volume, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @clean_help_dir, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @build_afni_Xlib, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @afni.run.me, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @T1scale, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ScaleVolume, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_Make_Spec_Caret, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL) Clean up some spacing; avoid single line 'if' conds; use unaliased rm. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @RetinoProc, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Reorder, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ROI_decluster, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Install_InstaCorr_Demo, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Install_ClustScat_Demo, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @GradFlipTest, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @ExamineGenFeatDists, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @Atlasize, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if'. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @2dwarper.Allin, level 2 (MINOR), type 0 (GENERAL) Avoid single line 'if' conds. To avoid badness in some (older?) tcsh versions. 15 Jun 2021, P Taylor, @1dDiffMag, level 2 (MINOR), type 0 (GENERAL) Put spaces in if-conditions after 'if' and before 'then'. To avoid badness in some (older?) tcsh versions.
14 Jun 2021, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 4 (BUG_FIX) turn off local signing in crorden/dcm2niix_console/makefile 14 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Space before 'then' in if-cond; also remove all exclamations in comments. Resolved *very* weird opt parsing on *some* old tcsh.
10 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) rename src/suma_suma.h to src/SUMA/SUMA_X_objs.h This is to avoid glorious case-insensitive name conflicts on Macs. As suggested by the merciful D Glen. 10 Jun 2021, RC Reynolds, SurfLocalstat, level 2 (MINOR), type 1 (NEW_PROG) add Ziad's program to the default build This is to allow use of the 'mode' stat. 10 Jun 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) New opt '-echo', for odd-behavior-on-other-systems-investigtion-purposes. Also print AFNI and program version numbers at top.
09 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 6 (ENHANCE) Changes to make T1-T1 alignment with lpa+ZZ more reliable Problem - aligning whole head volume to MNI template (top of head only) - alignment sometimes fails badly. This problem is much less common if source and base image coverage are compatible. If users will not zero out or chop off the sub-brainstem part of the head, then the following changes made to 3dAllineate will help: a) carry out a larger search in the coarse pass (more trials) b) eliminate 'ov' and 'mi' from lpa+ as these caused problems NOTE: 'ov' and 'mi' are still in lpc+ Also investigated why linux and macos results differ. Tracking optimizer leads to hypothesis that differences in roundoff error slowly accumulate, and then at some point powell_newuoa makes a step decision that can alter the optimizing trajectory significantly. There doesn't seem to be a good way to avoid this. However, with the chanes above, both macos and linux versions work reasonably well, and differ at most in about 2 mm (and that only in one case out of 38 whole head tests). 09 Jun 2021, RW Cox, 3dUndump, level 1 (MICRO), type 2 (NEW_OPT) Add -allow_NaN option To allow some DERANGED AFNI user whose name will not be mentioned to create a dataset containing NaN (Not A Number) floating point values.
08 Jun 2021, RW Cox, 3dQwarp, level 1 (MICRO), type 4 (BUG_FIX) Modify to make it work with 2D images again Had to fix THD_fillin_once to allow for special case of nz==1
03 Jun 2021, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 6 (ENHANCE) sync crorden/dcm2niix_console with repo, version v1.0.20210317 Thanks to C Rorden for suggesting the update.
02 Jun 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL) Undo previous tweak to auto_warp.py; back to using *.nii. Reverting, because AFNI_COMPRESSOR has been updated. 02 Jun 2021, P Taylor, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) Undo previous tweak to db_mod.py (for auto_warp.py); back to using *.nii. Reverting, because AFNI_COMPRESSOR has been updated.
01 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) AFNI_COMPRESSOR no longer affects NIFTI (seems AFNI_AUTOGZIP never did)
30 May 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL) Use *.nii.gz, not *.nii, because of current AFNI_COMPRESSOR = GZIP. With current AFNI_COMPRESSOR = GZIP, get problems; now, no more. 30 May 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) New opt '-use_gz' to output gzipped NIFTI even with '-suffix ..'. Part of updating auto_warp.py to use *.nii.gz, not *.nii. 30 May 2021, P Taylor, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) Tweak db_mod.py: prep for auto_warp.py to now always use *.nii.gz. Just mv *.nii.gz files, rather than *.nii, from auto_warp output dir.
29 May 2021, RC Reynolds, SurfLocalstat, level 1 (MICRO), type 2 (NEW_OPT) add 'mode' stat modal smoothing
24 May 2021, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Several small updates for convenience and organization: help updated... more QC images; split intermediate text desc; new cmd_log.
20 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Clean up exiting from help and version checking. Doesn't go via the verbose GOOD_EXIT route anymore, which it shouldn't.
19 May 2021, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) fix volreg TSNR computation in surface analysis (TSNR still in volume)
17 May 2021, DR Glen, lesion_align, level 3 (MAJOR), type 1 (NEW_PROG) Alignment for data with large lesions Developed for hemispherectomy and lobectomy data. May be applicable to stroke and smaller lesion data too
12 May 2021, P Taylor, @SUMA_Make_Spec_FS, level 1 (MICRO), type 0 (GENERAL) Remove old/unnecessary comment from help of -NIFTI opt. Referred to earlier misconcept (need even mat dims for anatomical dset).
11 May 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) 1dplot.py improved for backward compatability to Python 2.7. So, for task FMRI, individual stim label plots work again in Py2.7. 11 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Set env var to turn off NIFTI warnings. That is, AFNI_NIFTI_TYPE_WARN -> NO. 11 May 2021, P Taylor, 1dplot.py, level 1 (MICRO), type 0 (GENERAL) Replace str.isnumeric() with str.isdigit(), for backward compatability. Python 2.7 didn't have that method for str type.
10 May 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 2 (NEW_OPT) New opt: '-set_xhair_gap ..', to allow setting crosshair gap. Default value is -1.
06 May 2021, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE) Make -zskip work with -paired Rejecting any value pairs where either setA or setB is 0.
03 May 2021, P Taylor, 3dClusterize, level 1 (MICRO), type 0 (GENERAL) Add bracket to meta-text above table in case of abs value in table. Thanks, watchful AFNI user YurBoiRene.
01 May 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) fix niml.dset suffix in the case of -regress_compute_fitts on the surface Thanks to the all-seeing S Torrisi for noting the problem.
29 Apr 2021, P Taylor, 3dClusterize, level 2 (MINOR), type 2 (NEW_OPT) Forgot to actually add in the new opt for data scaling in last change... Now opt '-abs_table_data' is in the code. 29 Apr 2021, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX) 1) Now apply any scaling to 'data' in table (wasn't scaling, before). 2) Change table def: don't abs val Mean and SEM; use opt for that.
23 Apr 2021, P Taylor, 1dplot.py, level 2 (MINOR), type 2 (NEW_OPT) Can force ylabels to wrap at a certain num of chars (-ylabels_maxlen ..). For APQC, so long stimulus labels don't run into each other. 23 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) 1dplot.py improved, so stimulus labels on y-axis will wrap. Reduce/remove overlap of long stim labels.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 7 (REMOVE) This program has been superceded by: adjunct_apqc_tsnr_general. The new version is more... general. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 7 (REMOVE) This program has been superceded by: adjunct_apqc_tsnr_general. The new version is more... general. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 2 (NEW_OPT) More options from @chauffeur_afni here. Tryin' to make nicer images. 16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 1 (NEW_PROG) Made to replace adjunct_apqc_tsnr_with_mask and adjunct_apqc_tsnr_no_mask. Also expands/generalizes this functionality. 16 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Use newer adjunct_apqc_tsnr_general for TSNR images. Single/more adjunct general prog than previous separate ones. 16 Apr 2021, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 0 (GENERAL) Internal logic for making TSNR dsets tweaked. TSNR images in QC*/media/ dir get unique name, too (no change for user). 16 Apr 2021, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) New keyword EMPTY for '-topval ..' opt, make scripting easier. Corrected discrete cbar help example, too.
06 Apr 2021, RC Reynolds, ap_run_simple_rest.tcsh, level 3 (MAJOR), type 1 (NEW_PROG) run a quick afni_proc.py resting state analysis for QC
04 Apr 2021, DR Glen, @Atlasize, @MakeLabeltable longname fix, level 1 (MICRO), type 4 (BUG_FIX) Longnames not working in combination with labels fixed for atlases
24 Mar 2021, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT) -FWHMxyz allows different blurring amounts in different directions 24 Mar 2021, P Taylor, 3dBrickStat, level 3 (MAJOR), type 4 (BUG_FIX) Fix bug: having non-full-FOV mask + perc calcs affected other calcs. Calcs should now be consistent even with those opts used. Thanks, RCR. 24 Mar 2021, P Taylor, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) New opt: -is_atlas_or_labeltable. 1 if dset has an atlas or labeltable; otherwise, 0.
23 Mar 2021, P Taylor, 3dBrickStat, level 1 (MICRO), type 0 (GENERAL) Uniformize internal spacing. Should be no change in behavior. Just a few comments stretch far still.
16 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) simplify logic in THD_mask_erode(), with negligible slowdown 16 Mar 2021, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally. 16 Mar 2021, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally. 16 Mar 2021, P Taylor, @djunct_4d_imager, level 1 (MICRO), type 2 (NEW_OPT) Set env AFNI_COMPRESSOR to NONE. Avoid minor badnesses occasionally.
15 Mar 2021, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT) Add -wprefix option This option will write out the computed warp for each sub-brick. Mostly for Zhark's curiousity. 15 Mar 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 5 (MODIFY) Move help from main() to function Allin_Help() 15 Mar 2021, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT) add convenience options -perclist and -perc_quiet
13 Mar 2021, RW Cox, parser.f, level 1 (MICRO), type 4 (BUG_FIX) non-NUL terminated FORMAT string In Fortran-77, character strings are fixed length and filled out with blanks -- they are not NUL terminated as in C. In one place in parser.f, a variable FORMAT string is used (about line 709, string C_VAL) -- but that gets passed to an f2c library function that assumes NUL terminated string, and so a buffer overrun error can happen. This has never caused a crash or error, as far as I know, but was detected using the gcc -fsanitize=address option by Chris Rorden. To avoid possible error, the Fortran line above the use of this string FORMAT sets the last character of C_VAL to NUL. At the same time, changes were made to the f2c library headers to properly adapt to either 32 or 64 bit pointers. Formerly, the pointer size was fixed to 4 bytes. A long commentary here for a very small issue. 13 Mar 2021, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) distribute libXp.6.dylib, since XQuartz has stopped doing it Thanks to C Gaillard and others on the MB.
10 Mar 2021, RC Reynolds, lib_tsv.py, level 2 (MINOR), type 1 (NEW_PROG) new TSV class library, geared toward BIDS event files 10 Mar 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 2 (NEW_OPT) Add in more control features, so can apply in more cases. Basically just allowing more chauffeur control.
08 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) applying NIFTI scale_slope to dset must be after setting ADN_datum Previously, NIFTI scalars were applied only after a DSET_load(). Thanks to D Glen for reporting the issue. 08 Mar 2021, P Taylor, map_TrackID, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3ddot_beta, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dZipperZapper, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dTrackID, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dReHo, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dRSFC, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dROIMaker, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dNetCorr, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dMatch, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dLombScargle, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dDWUncert, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller. 08 Mar 2021, P Taylor, 3dAmpToRSFC, level 1 (MICRO), type 5 (MODIFY) I/O strings now up to THD_MAX_NAME length; requested by L Waller.
06 Mar 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. 06 Mar 2021, P Taylor, @fat_tract_colorize, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. And tweak help to be more useful. 06 Mar 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) Run a bit more quietly, setting ENV vars and GUI opts. Fewer warnings and messages. 06 Mar 2021, DR Glen, MNI HCP Glasser atlas regrid, level 1 (MICRO), type 4 (BUG_FIX) Move from grid of FreeSurfer 256^3 to match MNI 2009c grid. The FreeSurfer grid is zeropadded to 256 slices. All values remain the same, so essentially same atlas except memory requirements are less and easier to combine with template-based datasets. Also works better in Draw Dataset plugin because of the grid match. No source code changes, just a change in the pub/dist/atlases/current directory 06 Mar 2021, DR Glen, @AddEdge PBAR fix, level 1 (MICRO), type 4 (BUG_FIX) PBAR fix
05 Mar 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_cormat_warnings_full This version includes the baseline terms in the warning list. 05 Mar 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Have APQC copy the ss_review_basic text file into the QC dir. Might want this text info available for easy parsing at group level.
04 Mar 2021, RC Reynolds, 3dROIstats, level 2 (MINOR), type 4 (BUG_FIX) fix surprising slowness This would previously unload/mallocize/reload every time point, possibly to free completed data. Then NIFTI input would be re-read every time point (this might have changed due to something else). Instead, mallocize in the first place, not per time point. Also, avoid scaling floats by 1.0. Thanks to C Craddock for reporting the problem.
03 Mar 2021, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY) update dotfiles for 'complete' files before running apsearch Do this so apsearch will not tell users to update the dotfiles again. Thanks to D Glen. 03 Mar 2021, RC Reynolds, @clean_help_dir, level 2 (MINOR), type 5 (MODIFY) warn on any error in 'cat *.complete* > xx' commands In MacOS 11 Rosetta terminals, those commands are *sometimes* crashing. Warn on any such failure. Such a crash could cause trouble for other programs, too. Thanks to D Glen. 03 Mar 2021, P Taylor, gen_ss_review_scripts.py, level 2 (MINOR), type 0 (GENERAL) Add sswarper2 to name of recognized progs for getting template dset. Can get uvar for APQC for this top secret NL alignment prog. 03 Mar 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 4 (BUG_FIX) Had an early exit from earlier debugging. Ironic, really, that a debugging line became a bug. Go figure. 03 Mar 2021, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 4 (BUG_FIX) On one system an instrutable error message 'Unknown user: 1~.' occurred. This change (doublequote file name? remove EOL in backticks?) fixed it. 03 Mar 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) Make nice new WB mask, make some QC images of mask/segs/ROIs. Also make tables of ROI info (size stuff).
01 Mar 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Fix output dir of an intermediate QC image. The init*uaff* should now be in the usual QC/ dir.
27 Feb 2021, DR Glen, clang macos 11 M1-ARM mods, level 3 (MAJOR), type 0 (GENERAL) Makefile changes for ARM builds for new Macs Makefile, misc. changes for building for M1 27 Feb 2021, DR Glen, gap setting via plugout_drive, level 1 (MICRO), type 2 (NEW_OPT) Set the AFNI GUI crosshair gap with plugout_drive See README.driver for details 27 Feb 2021, DR Glen, atlas labels - remove trailing spaces, level 1 (MICRO), type 4 (BUG_FIX) Remove trailing spaces introduced by @Atlasize
25 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) With non-nonlinear warps, processing now goes all they way through. Bit more *.txt output, fixed mapping of anat follower non-ROI dset.
24 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add options -regress_extra_ortvec, -regress_extra_ortvec_labels Pass sets of regressors of no interest, to go into the baseline. Requested by multiple people, including Carolin31 on MB. 24 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Add more TSNR plotting: if vreg TSNR is calc'ed, or if no mask exists. Also a bug fix in HAVE_MASK definition; fix ranges in some plots. 24 Feb 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 1 (NEW_PROG) Now used in APQC to make TSNR plot. Has mostly required olay/ulay args, for when *no* mask exists.
23 Feb 2021, RW Cox, lots of them, level 1 (MICRO), type 0 (GENERAL) Changes to avoid compile warnings with -Wall option Mostly cosmetic fixes, but a few minor errors discovered and patched. About 50 .c files affected.
22 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) masking is no longer applied to TSNR dset; pass mask_dset to gen_ss Requested by P Taylor. 22 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) New part of regr block: TSNR plot. Shows brain slices. 22 Feb 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 1 (NEW_PROG) Now used in APQC to make TSNR plot. Has mostly required olay/ulay args, as well as mask. 22 Feb 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt: -pbar_comm_gen, for APQC. Also remove warning about ffmpeg unless using MPEG.
21 Feb 2021, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY) remove actual targets in RM for LIBMRI_* 21 Feb 2021, RC Reynolds, @djunct_glue_imgs_vert, level 1 (MICRO), type 5 (MODIFY) allow -help without deps, so move dependency tests
19 Feb 2021, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY) updates for ShowMode in SUMA_xColBar.c Resolve compiler warnings, but avoid logic changes at the same time as XQuartz beta issues. So temporarily keep original logic. Once we feel stable with XQuartz, look into expected fixes. Search for 'todo: apply ShowMode' in SUMA_xColBar.c.
18 Feb 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) warn about problematic version of XQuartz Bad versions seem to be 2.8.0_alpa*, 2.8.0_betas[12] (3+ okay?). With improvements we have seen, maybe we should warn on any beta.
17 Feb 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) moved AFNI_ijk_* protos from afni.h to 3ddata.h All thd_coords.c protos are in 3ddata.h now.
10 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL) More QC images: WM and GM tissue, solo. Thanks for suggestions, P Molfese. 10 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Add in -mask_ss option, to replace skullstripping with a mask. For example, using fs*mask*nii from @SUMA_Make_Spec_FS after FS.
09 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 0 (GENERAL) Add fractional volume info to the text file. This makes 2 new columns in the output *.1D files. 09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL) New column of ROI vol fraction, relative to fs_parc_wb_mask.nii.gz. This prog should always be run after adjunct_suma_fs_mask_and_qc. 09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL) Renamed, from adjunct_suma_rois_qc.tcsh. Removing extension. 09 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 0 (GENERAL) Make new mask dset from parcellation. Add new image of new dset. 09 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL) Renamed, from adjunct_suma_fs_qc.tcsh. Removing extension.
08 Feb 2021, RW Cox, AFNI gui, level 1 (MICRO), type 6 (ENHANCE) Add Mean/Sigma statistic to Button 3 popup in graph viewer Kind of a cheap TSNR check for raw data. 08 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG) Will add to @SUMA_Make_Spec_FS for automatic QC output. This makes *.1D files of voxel counts of parcellations and segs. 08 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG) Will add to @SUMA_Make_Spec_FS for automatic QC output. This makes images of the brain mask, tissue segs and parcellation.
07 Feb 2021, DR Glen, clang+gcc10 macos 10.15 mods, level 3 (MAJOR), type 4 (BUG_FIX) Lots of little code fixes to handle compiler warnings Makefile updated and some long outstanding issues fixed
05 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Add in more intermediate QC snapshots (intermed align): init*jpg Also add '-echo' opt for verbose terminal stuff.
03 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New QC image, of affine warping. Also pass along '-echo' opt to modal smoo/report script.
01 Feb 2021, P Taylor, 3dedge3, level 2 (MINOR), type 2 (NEW_OPT) Adding -automask (and -automask+X) functionality. Mainly to help with comparisons with 3dedgedog.
27 Jan 2021, RW Cox, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE) Enhance -PearSave option Now it works with -allcostX to give the LPC values at the start of the run, instead of only at the end. Now it works with any cost functional, say '-hel', instead of '-lpc' and '-lpa'. That is, you can get the local Pearson stuff even if it isn't actually used in the optimization. 27 Jan 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) New run script created (run_01*) in L_MAKE_DRIVE_SCRIPT block. Opens std.141*both*spec in SUMA and SurfVol in AFNI, and starts talking. 27 Jan 2021, P Taylor, 3dAttribute, level 2 (MINOR), type 0 (GENERAL) Update help to have fancy sections and more examples. Also provide link to README.attributes file, for user reference.
26 Jan 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 2 (NEW_OPT) New -PearSave option Saves the local Pearson correlations into a dataset at the end of an alignment. Mostly for visualization fun. 26 Jan 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) do not convert NIFTI scaled shorts to float If slope!=0 && inter==0, pass slope as brick_fac. Thanks to C Caballero and S Moia for reporting this.
11 Jan 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) AFNI graph viewer box labels now selectable from menu In the Colors, Etc. menu, new items were added to enable and control the labels used in Box mode. Keystroke ctrl-B cycles between all Data modes. In addition, labels can now be drawn for graph matrix size up to 9x9.
03 Jan 2021, RC Reynolds, SurfMeasures, level 2 (MINOR), type 5 (MODIFY) shift memory allocation/free around, mostly to match libSUMA Inspired by C Rorden via sanitizer warnings.
31 Dec 2020, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) modify help: be more clear about bandpassing being undesirable Also, add example of high-pass filter to model slow drift. See help for option -regress_polort.
29 Dec 2020, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with nifti_clib 29 Dec 2020, RC Reynolds, nifti_tool, level 1 (MICRO), type 6 (ENHANCE) add help example for creating a new dataset given a raw data file
22 Dec 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fixed 6 copy-and-paste errors using MRI_TYPE_maxval Thanks to C Rorden for bringing this up and suggesting code fixes. 22 Dec 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New default feature_size: 0.5. (Old default: was unset). Made almost no dif in mac demo, but should be slightly more robust, in gen . 22 Dec 2020, P Taylor, 3dmaskave, level 2 (MINOR), type 4 (BUG_FIX) MRI_TYPE_maxval fixed for byte case-- thanks, C Rorden! Same fix applied in: plug_maskave.c and thd_makemask.c.
21 Dec 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX) The '-orient ..' opt wasn't working-- that has been fixed. Now user can specify table coords with this opt. 21 Dec 2020, P Taylor, 3dROIMaker, level 1 (MICRO), type 0 (GENERAL) Tweak internal handling of reading inputs, prohibit hanging args. Now, hanging args should produce error (not just be silently ignored). 21 Dec 2020, P Taylor, 3dClusterize, level 1 (MICRO), type 0 (GENERAL) Tweak internal handling of reading inputs, prohibit hanging args. Now, hanging args should produce error (not just be silently ignored).
17 Dec 2020, RC Reynolds, 1dBport, level 1 (MICRO), type 4 (BUG_FIX) guard against silent failure of int overflow for ftop
01 Dec 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Tweaked default temp 'junk' filename to avoid low-probability badness New opt '-tmp_name_nice' for, well, read opt name. Improved help, too.
12 Nov 2020, P Taylor, fat_proc_connec_vis, level 1 (MICRO), type 0 (GENERAL) Set some env vars at top of script to turn off compression. Was causing odd error in one case.
06 Nov 2020, P Taylor, adjunct_tort_read_dp_align.py, level 2 (MINOR), type 1 (NEW_PROG) Script to read TORTOISE-DIFFPREP *_transformations.txt files. Puts them into usable order for calc'ing enorm and plotting mot/pars. 06 Nov 2020, P Taylor, adjunct_tort_plot_dp_align, level 2 (MINOR), type 1 (NEW_PROG) Script (tcsh) to translate TORTOISE-DIFFPREP *_transformations.txt files Wraps new adjunct_tort_read_dp_align.py and 1dplot* to make plots.
02 Nov 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Can now output SVG files, and can use newline chars in labels. Had to deal with newline escape seq internally.
28 Oct 2020, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL) Extra QC image: initial overlap of source and base dsets. Should help to know, in case anything goes awry later. 28 Oct 2020, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL) Extra QC image: initial overlap of T1w and T2w dsets. Should help to know, in case anything goes awry later.
19 Oct 2020, P Taylor, @djunct_overlap_check, level 3 (MAJOR), type 1 (NEW_PROG) Make of overlap of 2 datasets (esp for pre-align check, AW or SSW). Will make both non-obl and 3dWarp-deob'ed images of olap (and report). 19 Oct 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Simplifying output dir: Phase II and III. Thanks again, B Jung! New intermediate dir, animal_outs update, helpfile rewritten. 19 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Added new QC image to QC/ dir: initial source-base alignment. If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report. 19 Oct 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Added new QC image: initial source-base alignment (@djunct_overlap_check) If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report.
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Simplifying output dir: Phase I. Thanks, Ben Jung, for good suggestions! Put report*1D in QC/, and do*.tcsh and surfaces_* in new surfaces/ dir. 16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Add in status checks after many afni progs, to exit at/near first failure. Should be no change in output for users (in successful runs). 16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX) Now, first cp+resample src to RAI; else, shft is bad for non-xyz orients. Output warps can still apply to original orient dset fine.
29 Sep 2020, RC Reynolds, 3dANOVA3, level 1 (MICRO), type 6 (ENHANCE) be specific about limits for 'param must be in' error messages
24 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) Put in status checks through script to exit with error if any step fails. Should provide nicer behavior if something gang agley.
17 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX) fix use of platform.mac_ver (was there a change?)
16 Sep 2020, DR Glen, atlas label range selector, level 1 (MICRO), type 4 (BUG_FIX) atlas labels not interpreted in range selector properly atlas labels caused crash if selected in angle brackets on cmdline. Also allowed for spaces in atlas labels by replacing with underscores in command line.
15 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) whine if .zshrc references all_progs.COMP.bash; backup for distro
14 Sep 2020, RC Reynolds, apsearch, level 2 (MINOR), type 6 (ENHANCE) create complete.zsh files - like bash ones, but cleaned a little 14 Sep 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) update .zshrc: set PATH and DYLD_L_P..., and source all_progs.COMP.zsh
10 Sep 2020, DR Glen, Driving AFNI to get values, level 2 (MINOR), type 6 (ENHANCE) Drive AFNI to get current value in OLay, Threshold or ULay+ Can also get ULay and OLay prefixes
02 Sep 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) add options -show_field and -show_field_names Using the new -show_field option, for each entry one can show: - the full entry (as before) - only the first/main line - only the program name, or date, or author, etc. 02 Sep 2020, P Taylor, @SkullStrip_TouchUp, level 2 (MINOR), type 0 (GENERAL) Replace '-e' at top with several later status checks; 'exit 0' after help. No effect on output, except being more general.
01 Sep 2020, P Taylor, fat_roi_row.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_proc_grad_plot, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution. Already have a better one (with fewer dependencies!) ready to go. 01 Sep 2020, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mvm_review.py, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution. This program never even made it to full beta status. 01 Sep 2020, P Taylor, fat_mvm_prep.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mvm_gridconv.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 6 (ENHANCE) Update to run in Python 3 (using 2to3, plus extra tweaks). Should now run in both Python 2 and 3. 01 Sep 2020, P Taylor, fat_lat_csv.py, level 2 (MINOR), type 7 (REMOVE) Remove program from distribution, with lib: lib_fat_Rfactor.py. R deps are a mess between Py2 and Py3; might rewrite better in future. 01 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX) If '-skipwarp' was used, crashed at very end (sigh). Fixed that crash behavior; no changes in outputs.
31 Aug 2020, RC Reynolds, afni_python_wrapper.py, level 1 (MICRO), type 2 (NEW_OPT) add -joinn for list output; add list_intersect and list_diff funcs
27 Aug 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 1 (MICRO), type 6 (ENHANCE) set up for alternatively building without SUMA 27 Aug 2020, RC Reynolds, @diff.tree, level 1 (MICRO), type 4 (BUG_FIX) better handling of missing trailing directory args 27 Aug 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 5 (MODIFY) Well, usage+output shouldn't really change, but it should be more stable. There is also a new opt: -align_centers_meth (read the help).
26 Aug 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 6 (ENHANCE) much limiting of line lengths to 80 chars - should be no real change 26 Aug 2020, RC Reynolds, ClustExp_StatParse.py, level 1 (MICRO), type 6 (ENHANCE) python 3 update to decode() subprocess output 26 Aug 2020, P Taylor, @animal_warper, level 1 (MICRO), type 4 (BUG_FIX) Fix case of running prog with no args. Should show help; now it DOES show help, with no error.
25 Aug 2020, RC Reynolds, sqwave, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, siemens_vision, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, plug_3ddup.so, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, mritopgm, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, mayo_analyze, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use nifti_tool 25 Aug 2020, RC Reynolds, lpc_align.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, ge_header, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, ftosh, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, ent16, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, check_dset_for_fs.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use afni_proc.py 25 Aug 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added new types TYPE_REMOVE and TYPE_REINSTATE This is to track when programs or notable functionality gets removed. 25 Aug 2020, RC Reynolds, abut, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Xphace, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Ifile, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, FD2, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use afni 25 Aug 2020, RC Reynolds, DoPerRoi.py, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, Dimon1, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use Dimon 25 Aug 2020, RC Reynolds, AlphaSim, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dClustSim 25 Aug 2020, RC Reynolds, @snapshot_volreg3, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use @snapshot_volreg 25 Aug 2020, RC Reynolds, @make_stim_file, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use timing_tool.py 25 Aug 2020, RC Reynolds, @auto_align, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, @UpdateAfni, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use @update.afni_binaries 25 Aug 2020, RC Reynolds, @DTI_studio_reposition, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dttest, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dttest++ 25 Aug 2020, RC Reynolds, 3dproject, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dnoise, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dfim, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dDeconvolve 25 Aug 2020, RC Reynolds, 3ddup, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dbuc2fim, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dWavelets, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dUniformize, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dUnifize 25 Aug 2020, RC Reynolds, 3dProbTrackID, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dTrackID 25 Aug 2020, RC Reynolds, 3dMax, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dBrickStat 25 Aug 2020, RC Reynolds, 3dICC_REML.R, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dFourier, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dBandpass 25 Aug 2020, RC Reynolds, 3dFWHM, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dFWHMx 25 Aug 2020, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dDeconvolve 25 Aug 2020, RC Reynolds, 3dCountSpikes, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dToutcount 25 Aug 2020, RC Reynolds, 3dAnatNudge, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use align_epi_anat.py 25 Aug 2020, RC Reynolds, 3dAOV.R, level 2 (MINOR), type 7 (REMOVE) removed from distribution 25 Aug 2020, RC Reynolds, 3dANALYZEtoAFNI, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 3dcopy or to3d 25 Aug 2020, RC Reynolds, 1dDW_Grad_o_Mat, level 2 (MINOR), type 7 (REMOVE) removed from distribution - use 1dDW_Grad_o_Mat++
21 Aug 2020, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX) Fix header deps of underlying progs (namely, readglob.c). Was crashing on some NIML reading cases.
09 Aug 2020, DR Glen, @ROI_decluster, level 2 (MINOR), type 1 (NEW_PROG) Remove small clusters or single voxels in datasets with many ROIs Keeps only the largest part(s) of the ROI with adjustable threshold. Used for datasets with many ROIs, like those found in an atlas. Can be used in combination with @ROI_modal_grow

auto-generated by afni_history on Aug 5 2022