AFNI HISTORY

level 1 and higher

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


generated via the command : afni_history -html -reverse -min_level 1 -past_months 6 

---- log of AFNI updates (most recent first) ---- 17 Oct 2019, RC Reynolds, Makefile.*, level 1 (MICRO), type 4 (BUG_FIX) for strcasestr, we need to define _GNU_SOURCE 17 Oct 2019, RC Reynolds, 3dTcorr1D, level 1 (MICRO), type 4 (BUG_FIX) strcasestr fix subsumed by adding _GNU_SOURCE to make Undo removal of strcasestr. 17 Oct 2019, RC Reynolds, 3dANOVA, level 1 (MICRO), type 6 (ENHANCE) improve descriptions of some option errors to the user 17 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Display AFNI Tips in the terminal, via new opt: -show_tips. Will be used+parsed for the HTML RST docs.
16 Oct 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 6 (ENHANCE) re-insert updates from 2019.05.29, plus updates for -init_xform 16 Oct 2019, RC Reynolds, TwotoComplex, level 1 (MICRO), type 6 (ENHANCE) process entire time series, rather than just first volume(s) Done to further the quest of A Khojandi for world domination. 16 Oct 2019, RC Reynolds, 3dFFT, level 1 (MICRO), type 6 (ENHANCE) process entire time series, rather than just the first volume Done for A Khojandi.
15 Oct 2019, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX) -bysub fix Methods 1 and 2 can conflict, and the choice is arbitrarily made to favor Method 1 when the input matches both situations. 15 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -subbrick_info, to write only 'At sub-brick #N' info to stdout
11 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) checked and merged another 17 commit PR from pn2200 This is mostly to resolve missing prototypes.
10 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -niml_hdr, to write full NIML header(s) to stdout 10 Oct 2019, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX) search for niml.dset errts datasets 10 Oct 2019, RC Reynolds, afni_base.py, level 1 (MICRO), type 4 (BUG_FIX) in NIML case, exist should check ppv file directly
09 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) checked and merged 30 commit PR from pn2200 This is mostly to resolve compiler warnings.
07 Oct 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) probably the last set of test updates for now 07 Oct 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Change text of animal_outs.txt. Minor 'under the hood' changes, too. 07 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Simpler opts for package and version number. For scriptability.
04 Oct 2019, RC Reynolds, 3dNLfim, level 1 (MICRO), type 4 (BUG_FIX) allow for longer input and output file names Names were malloc'd with MAX_NAME_LENGTH; use nifti_strdup, instead. Thanks to S Wardle for bringing this to light.
03 Oct 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 0 (GENERAL) Just divvied up the behavior of the functions better. Also have a general, NxN case . 03 Oct 2019, P Taylor, epi_b0_correct.py, level 1 (MICRO), type 0 (GENERAL) Calculate oblique transform differently; use 3dWarp instead of cat_matvec. Probably negligible practical change. 03 Oct 2019, P Taylor, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) Fancy new function to calculate if a list-matrix is square. ps: not that fancy.
02 Oct 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) The naming convention of PE dist dir has been reversed; mask opts changed. PE dist dir should match with JSONs better; 3dmask_tool does masking now. 02 Oct 2019, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 0 (GENERAL) Output more specific information about finding unexpected negative values. Tell user the [row, col] of potentially bad values, for easier QC.
30 Sep 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) added test scripts under commands, along with cmake versions for build
26 Sep 2019, RC Reynolds, NIFTI, level 1 (MICRO), type 5 (MODIFY) nifti_read_ascii_image no longer closes fp or free's fname
23 Sep 2019, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX) missed endif Thanks to A Winkler for noting the problem.
18 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) if -html_review_style pythonic, check for matplotlib
16 Sep 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) check on /usr/local/bin/python* files, as is done with /sw/bin
13 Sep 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) report XQuartz version As suggested by P Taylor. 13 Sep 2019, P Taylor, 3dWarp, level 2 (MINOR), type 2 (NEW_OPT) New opt: -disp_obl_xform_only. Better way to get transform between obl coords than cat_matvec trickery.
12 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) add file tracking and -show_tracked_files option In preparation for shifting evil for P Taylor and D Glen. 12 Sep 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) Output QC directory of images now, as well. Useful for quick QC. Later, will add some checks for obl, to not smooth unnec. 12 Sep 2019, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) Use 'mkdir -p' with odir now. Simplifies scripts using it.
10 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Unifize output in standard space. Better for visualization in afni_proc.py QC. 10 Sep 2019, P Taylor, epi_b0_correct.py, level 1 (MICRO), type 0 (GENERAL) Fix help descriptions (thanks L. Dowdle for fixes). Also add '-hview' capability.
09 Sep 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) add control for 3dDespike -NEW25 Requested by aparekh on the Message Board.
06 Sep 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Two minor changes: montages now separated by 1 gap line. ... and show censor bars in VR6 plots, if censoring. 06 Sep 2019, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Now use montgap=1 by default. This is for APQC applications, where subj data fills FOV. 06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Output skullstripped version of template in std space. Also add 'notes' to that file, so gen_ss*script* can find template. 06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Put QC images into subdir called QC; output mask. Few other tiny changes/reorganizations internally.
05 Sep 2019, RC Reynolds, SurfMeasures, level 1 (MICRO), type 5 (MODIFY) retab and fix indentations
04 Sep 2019, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 6 (ENHANCE) check for valid 'mris_convert --help' output 04 Sep 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opts: -obl_resam_ulay OIU, -obl_resam_Olay OIO, -obl_resam_box OIB. Control resampling of dsets (ulay, olay, focus box) when applying obl. 04 Sep 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-extra_fs_dsets ..', to translate more FS-created surf/ dsets. Allow more FS surf dsets to be brought into SUMA. For F. Lalonde.
03 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) New QC imaging with @chauffeur_afni; mask created, too. And a few minor changes under the hood, worked out with DRG.
31 Aug 2019, DR Glen, @animal_warper,@FindAfniDsetPath, level 1 (MICRO), type 4 (BUG_FIX) better full_path option for paths with ../ More use in animal_warper for templates and atlases 31 Aug 2019, DR Glen, @animal_warper, level 1 (MICRO), type 2 (NEW_OPT) -keep_temp to keep temporary files and awpy directory 31 Aug 2019, DR Glen, @animal_warper, level 1 (MICRO), type 4 (BUG_FIX) follower fixes 31 Aug 2019, DR Glen, @FindAfniDsetPath, level 1 (MICRO), type 2 (NEW_OPT) full_path option - full path for current path
30 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 4 (BUG_FIX) Fix input opt to change blur size; was broken before, crashing prog. Thanks, L. Dowdle for finding! 30 Aug 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opts: -edge_enhance_ulay EE, -obliquify OBL. Different way to enhance edges of ulay, and apply obliquity info. 30 Aug 2019, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) supersize supersize - larger range of scaling for smaller animals to template 30 Aug 2019, DR Glen, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT) more options+fixes AFNI view reset for NIFTI feature_size and supersize options for smaller animals
29 Aug 2019, P Taylor, @auto_tlrc, level 3 (MAJOR), type 0 (GENERAL) RE-introducing the program '@auto_tlrc' to the distribution. It had been mistakenly deleted somehow. 29 Aug 2019, P Taylor, lib_gershgorin.py, level 1 (MICRO), type 0 (GENERAL) Updated to change way aff12.1D files were read. No change in calculated outputs. 29 Aug 2019, P Taylor, afni_util.py, level 1 (MICRO), type 0 (GENERAL) Remove function: read_aff12_to_mat34(). 'Twas unnecessary. 29 Aug 2019, DR Glen, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT) slew of options ok_to_exist for restarts, template and segmentation output prefixes, rigid/rigid_equiv/affine/all alignment, follower data
28 Aug 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 1 (NEW_PROG) Funcs to answer question: is this aff12 matrix very different from I? Uses fun algebraic facts known to and shared by the inimitable RWC. 28 Aug 2019, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) Matrix-y things: read_aff12_to_mat34(), matrix_multiply_2D(). And supplements: matrix_sum_abs_val_ele_row(), calc_zero_dtype().
27 Aug 2019, RW Cox, 3dREMLfit, level 1 (MICRO), type 6 (ENHANCE) Allow reading -matim matrix from a FIFO instead of a file For some reason, NIML doesn't like treating a FIFO as a file: stream. 27 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) linux_fedora_28_shared: make libf2c.so as a shared object 2.4 GB binaries -> (libmri.so) 600 MB -> (libSUMA.so) 202 MB -> (libf2c.so) 190 MB 27 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 0 (GENERAL) Added more fields to the output param text file. Also added to the help file (including *about* the params text file). 27 Aug 2019, P Taylor, 3dSpaceTimeCorr, level 2 (MINOR), type 2 (NEW_OPT) New opts: '-freeze* ..' that allow one to fix a location in dset A. Input for Zhihao Li.
26 Aug 2019, RW Cox, mri_read_1D, level 1 (MICRO), type 6 (ENHANCE) Modify to allow reading from a named pipe (FIFO) You can't seek/rewind on a FIFO, so have to use special code - adapted from the mri_read_1D_stdin function. 26 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) linux_fedora_28_shared: make libSUMA.so as a shared object 2.4 GB binaries -> (libmri.so) 600 MB -> (libSUMA.so) 200 MB 26 Aug 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) report 'R RHOME' 26 Aug 2019, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) check for dyn.load error via 3dMVM 26 Aug 2019, P Taylor, @chauffeur_afni, level 1 (MICRO), type 2 (NEW_OPT) New opt, '-ulay_comm': provide comment on ulay vals in pbar json. Also, saving ulay min/max in pbar json is new behavior.
23 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) updates corresponding to Travis CI OS change: Ubuntu 14->16 Set .travis.yml to use OS_notes.linux_ubuntu_16_64 for system udpate, and update the notes to include fix of GLwDrawA.h. Also, seem to need to enable mysql. 23 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 4 (BUG_FIX) Fixed calculation when PE effective echo spacing is input. The conversion to BWPP was wrong; led to almost no distortion corr. 23 Aug 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt, '-edgy_ulay': can turn ulay into edge-ified version of itself. Useful for showing alignments.
22 Aug 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) After 25 years, replace image false color with Google Turbo! Instead of AJJ's old color spectrum from FD, which had way too much green. 22 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) (w/dglen) thd_gifti: remove INDEX_LIST DA from from list When converting a GIFTI dataset to NIML, any index list should be separated early, so as not to affect the SPARSE_DATA NIML element. Thanks to T Holroyd for noting the problem. 22 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) THD_write_atr(): make the Kris K condition do more aggressive napping More aggressive napping?!? Sleep 6 times for 2^(n+1) seconds, up to ~1 min, for a total of ~2 min.
21 Aug 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 6 (ENHANCE) Add Google Turbo colormap
20 Aug 2019, RW Cox, 3dREMLfit, level 1 (MICRO), type 6 (ENHANCE) Make attribute names in matrix file be insensitive to case 20 Aug 2019, RW Cox, 3dPval, level 1 (MICRO), type 2 (NEW_OPT) Add -zscore option 20 Aug 2019, P Taylor, @SUMA_Make_Spec_FS, level 1 (MICRO), type 0 (GENERAL) Indent properly-- loops/conditions were too hard to follow. Should have no change in output but facilitates code editing.
19 Aug 2019, RW Cox, 3dTshift, level 1 (MICRO), type 2 (NEW_OPT) -wsinc5 and -wsinc9 options Interpolation in time introduces autocorrelation. This effect is not appreciable for Fourier (FFT) interpolation, but is noticeable for the polynomial methods. Plus/minus 5 and 9 weighted sinc interpolation options were added to test if these would reduce this artifact. The answer is that wsinc5 is better than heptic, but it is still visible; wsinc9 pretty much eliminates it inside the brain, but it is visible in the low-signal region outside the brain. 19 Aug 2019, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 4 (BUG_FIX) matrix_f.[ch]: dupe matrix_augment_01_columns from matrix.[ch] When choosing between more local functions and those included in a linked library, some systems seem to go all-or-nothing for one file at a time. So for 3dDeconvolve_f, matrix_f.c needs everything that might come from matrix.c. Otherwise we should have matrix_f.h rename all of those functions, to avoid relying on compiler choices. 19 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) Makefile.INCLUDE: add libmri target, for build system Let the make system decide whether it should be a shared lib. Also, make install_plugins just plug*.so model*.so and have itall target depend on install_lib.
16 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) (w/dglen) in THD_write_atr(), give file opening multiple opertunities Done for K Knutson. 16 Aug 2019, JK Rajendra, FATCAT_matplot, level 1 (MICRO), type 4 (BUG_FIX) Fix for FATCAT_matplot header reading.
15 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) build R_io.so with usable link to libmri.so Modify Makefile.linux_fedora_28_shared and Makefile.INCLUDE to control creation of Makevars via R_IO_MODIFY_LINUX. 15 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL) add other_builds/OS_notes.linux_fedora_30.txt Works with Makefile.linux_fedora_28_shared. 15 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL) This program has been pretty fully revamped, and might be worth using now. New scaling from Vinai, several updates/fixes/changes from last ver. 15 Aug 2019, DR Glen, @animal_warper, level 3 (MAJOR), type 1 (NEW_PROG) Warp data to template and atlas segmentation to subject Tested for macaques. Derived from macaque_align.csh and NMT_subject_align.csh
14 Aug 2019, DR Glen, @FindAfniDsetPath append_file, level 2 (MINOR), type 2 (NEW_OPT) Append file name to path with -append_file option Useful for atlas names to full dataset names and other scripting purposes
13 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX) fix -VXXXX= for real operating systems 13 Aug 2019, RC Reynolds, RetroTS.py, level 1 (MICRO), type 0 (GENERAL) RVT_from_PeakFinder.py: remove unused plot() 13 Aug 2019, DR Glen, whereami atlas dataset, level 2 (MINOR), type 2 (NEW_OPT) return dataset given atlas name(s) Print atlas dataset for each input atlas whereami -atlas TT_Daemon -show_atlas_dset prints TTatlas+tlrc each -atlas atlasname prints the corresponding atlas dataset 13 Aug 2019, DR Glen, @FindAfniDsetPath atlas name search, level 2 (MINOR), type 5 (MODIFY) Search SUPP_ATLAS_DIR path and look for atlases by name Search additional directory for extra atlases and by name Can search for TT_Daemon (atlas name) or TTatlas+tlrc (atlas dataset)
12 Aug 2019, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) python3 compatibility Including: make_stim_times.py, python_module_test.py, lib_matplot.py, slow_surf_clustsim.py, lib_surf_clustsim.py, make_pq_script.py.
08 Aug 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE) be more merciful in the case of timing overlap - ISI stats: allow and adjust for stim overlap - dur stats: show file/condition with stats - match output between python2 and python3
07 Aug 2019, RC Reynolds, rPkgsInstall, level 2 (MINOR), type 6 (ENHANCE) more programs that need R_LD_LIBRARY_PATH Full list: 1dRplot, 3dICC, 3dISC, 3dLME, 3dMEMA, 3dMEPFM, 3dMVM, 3dPFM, 3dRprogDemo, 3dSignatures, ExamineXmat, MBA, RBA, rPkgsInstall.
05 Aug 2019, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) check for matplotlib.pyplot 05 Aug 2019, RC Reynolds, 3dMVM, level 2 (MINOR), type 5 (MODIFY) set R_LD_LIBRARY_PATH for all 3d* R-calling programs using $afpath on osx For macs: to allow R_io.so to load shared libraries needed by libmri, set the search path to include the abin, flat_namespace and R lib dir. This might apply to linux with libmri.so, as well. Thanks to N Adleman, C Caballero and E Silson.
01 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 0 (GENERAL) Rename internal vars and opt names. Improving internal notation-- still very much a beta program version.
30 Jul 2019, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 6 (ENHANCE) format help output for sphinx conversion
29 Jul 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX) Reduce colorization interpolation problem When using discrete panes, conversion to 'continuous' colorscale causes a problem right at the boundary. This change reduces this problem. 29 Jul 2019, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE) format help output for sphinx conversion
26 Jul 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) add -make_backup and -echo Suggested by J Rajendra.
25 Jul 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -volreg_warp_master, for controlling the output grid Added for Y Miyawaki. 25 Jul 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 1 (NEW_PROG) Program to apply freq volume to EPI for B0 distortion correction. An honor to translate this program from one by Vinai Roopchansingh!
24 Jul 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_tsv_label_details option
23 Jul 2019, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE) add -tsv_labels option help and examples 23 Jul 2019, P Taylor, 1dplot.py, level 1 (MICRO), type 0 (GENERAL) Allow PDFs to be output directly. User just needs '.pdf' file extension on prefix.
22 Jul 2019, DR Glen, @Install_D99_macaque,NIH_Marmoset, level 2 (MINOR), type 4 (BUG_FIX) download script bugs tar platform differences and filename updates
19 Jul 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 6 (ENHANCE) add use of HDR/NIM_SLICE_TIMING_FIELDS for -field option This allows -{disp,diff}_{hdr,nim} an easy specification of fields related to slice timing. 19 Jul 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) if template is multi-volume, get vol [0] for group_mask Thanks to S Tumati for noting the problem.
18 Jul 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) look for multi-echo data in find_tcat 18 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Hadn't merged in updated library functions, so apqc_make_tcsh.py crashed. Updated library file in distribution now. 18 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 4 (BUG_FIX) Used to crash if output dir was PWD. Now fixed.
17 Jul 2019, RW Cox, AFNI gui, level 2 (MINOR), type 6 (ENHANCE) changes to make alpha and boxed (A and B) work with color panes People from Wisconsin are trouble. 17 Jul 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX) another fix for 32-64 bit NIFTI update for older xorg7 systems In thd_niftiread.c, cast nim->nz as int for EDIT_dset_items(). Newer C libraries seem to handle the possibility of 8 bits better, but we are reading as 4. Thanks again to R Birn. 17 Jul 2019, RC Reynolds, NIFTI, level 1 (MICRO), type 4 (BUG_FIX) fix inappropriate 'dimensions altered' warning on xorg7 Warning: dimensions altered since AFNI extension was added Use PRId64 for 64-bit int printing, works on old systems, too. Thanks to R Birn for noting the problem. 17 Jul 2019, P Taylor, apqc_make_html.py, level 1 (MICRO), type 0 (GENERAL) Minorest of changes to closing message. No more double slash. Wow.
16 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Fix incompatability with py2. Sigh.
15 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Add in obliquity values in vorig QC block. Also simplify text of radcorr block (fewer lines, less unnec repetition).
11 Jul 2019, RW Cox, 3dDeconvolve 3dREMLfit, level 1 (MICRO), type 3 (NEW_ENV) AFNI_INDEX_PREFIX changes '#' in sub-brick labels
10 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Can have text in the image tables now. Facilitates labelling, commenting, etc.
09 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Allow for multiple scripts to be executed, run and combined into 1 page. Single script tarball, single RST, can have multiple scripts/reflinks.
08 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Allow wildcard chars in IMAGE descrip; SUBSECTIONS added. Minor tweaks for formatting help files. 08 Jul 2019, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL) New default: '-do_clean' behavior on by default (clean up temp dir). New opt to not clean: -no_clean. -do_clean is fine to use, just boring.
05 Jul 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) (useless) switch to 3dTcorr1D for dot product Drops 2 commands down to 1 for computing corr_* volumes.
03 Jul 2019, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY) let X.stim.xmat.1D be empty for non-task case 03 Jul 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) if no stim, create sum_baseline.1D, rather than sum_ideal.1D 03 Jul 2019, RC Reynolds, 3dvolreg, level 1 (MICRO), type 4 (BUG_FIX) make 'second -zpad option' warning appropriate again 03 Jul 2019, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 4 (BUG_FIX) allow writing of empty stim files ($status 0) 03 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Expanded vstat QC block capabilities. Other tweaks, QC block IDs now in titles.
02 Jul 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) create X.stim.xmat.1D via 1d_tool.py -write_xstim, to keep labels
01 Jul 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) add complex Example 13; add use of @SSwarper outputs in Example 11 01 Jul 2019, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Labels on stim regressors, vorig QC block added, grayplot pbvorder/enorm. Help updated; output stats still if not align/tlrc blocks used. 01 Jul 2019, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL) Some minor tweaks to APQC HTML: better pbar size control, spacing. Also can interpret pbar text more broadly. 01 Jul 2019, P Taylor, dsetstat2p, level 1 (MICRO), type 1 (NEW_PROG) Complement of p2dsetstat. Convenience tool for converting a dset's stat to a p-value. 01 Jul 2019, P Taylor, @djunct_glue_imgs_vert, level 1 (MICRO), type 1 (NEW_PROG) New prog for APQC HTML stuff. Glue two images together vertically. Used when pixel x-dimensions match (mainly for APQC HTML). 01 Jul 2019, P Taylor, @chauffeur_afni, level 1 (MICRO), type 2 (NEW_OPT) New option '-pbar_for ..', which is mainly for APQC HTML. Can add a dict entry to txt file accompanying pbar output.
28 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) add vr_base_dset uvar
27 Jun 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -write_with_header and -write_xstim
26 Jun 2019, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) New opt '-weight_ts WTS' to multiply ROI ave time series. Input at the behest of Colm C. May it pour forth wondrous results.
25 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) get TSNR on surface 25 Jun 2019, P Taylor, 3dSkullStrip, level 3 (MAJOR), type 5 (MODIFY) Dset orient should no longer affect results (b/c of var of init cond). Intermediate resampling now reduces/removes var due to start.
20 Jun 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 4 (BUG_FIX) Use the CAPTION feature on image tables in text blocks. Also fix help display.
19 Jun 2019, RW Cox, afni GUI, level 1 (MICRO), type 4 (BUG_FIX) AFNI_PBAR_THREE mode didn't allow proper change of the panes Problem: code to put labels on the panes being invoked when it shouldn't be. Ugh. Who wrote this code, anyway? They should be SHOT!! 19 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) add surf_vol uvar 19 Jun 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) actually fail for some inappropriate blur options with surface analysis 19 Jun 2019, P Taylor, @djunct_make_script_and_rst.py, level 1 (MICRO), type 1 (NEW_PROG) New prog for Sphinx doc generation (well, assistance). Somewhat simple markup scheme used to generate RST, images and scripts.
18 Jun 2019, RW Cox, @SSwarper, level 1 (MICRO), type 6 (ENHANCE) Add 3dAutomask step for an extra cleanup 18 Jun 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) no mask if TSNR on surface Thanks to K Dembny for noting the problem. 18 Jun 2019, RC Reynolds, 3dGrayplot, level 1 (MICRO), type 6 (ENHANCE) allow grayplot of surface data if not -peelorder
17 Jun 2019, RW Cox, 3dmerge, level 1 (MICRO), type 2 (NEW_OPT) -1blur3D_fwhm Restores the ability to order differential amounts of blurring along the 3D axes of the dataset.
14 Jun 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add Makefile.linux_fedora_28_shared, to distribute a shared lib package This uses libmri.so, though other libraries should be added (SUMA). R programs do not yet work, as linking for R_io.so needs to be fixed. 14 Jun 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) add -hostname and -distdir This is to allow places to mirror some of the AFNI site.
13 Jun 2019, RC Reynolds, afni_base.py, level 1 (MICRO), type 6 (ENHANCE) allow for enclosed variables in afni_name, e.g. '${subj}'
12 Jun 2019, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) better prep for shared build, and fix shared build of suma_gts_progs Move mri_render.o out of libmri (corresponds with plug_render.so).Still ne ed to fix mpeg_encode.
10 Jun 2019, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY) apply FreeBSD patches from J Bacon - afni_xml.h: include inttypes.h - prf_common_circular.c: use malloc_stats_print() - Makefile.ptaylor.INCLUDE: add -fopenmp for building 3dDWUncert
06 Jun 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 3 (NEW_ENV) AFNI_OPACITY_LOCK YES = Locks the opacity (1-9) arrows between all image viewers. This is set to YES by default, and can be set to NO to get the old (unlocked) behavior. 06 Jun 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 5 (MODIFY) Change threshold scale upper limit selector from '**' to '10^' For DRG, and he owes me now. 06 Jun 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 4 (BUG_FIX) Different fix for the threshold scale size problem :( 06 Jun 2019, RW Cox, 3dTproject, level 1 (MICRO), type 6 (ENHANCE) Make sure time series mean is removed after projection To keep unruly users quiet(er). 06 Jun 2019, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 5 (MODIFY) back off recent updates - need to resolve -init_xform Thanks to H Keren for letting us know of the problem.
05 Jun 2019, P Taylor, 3dTrackID, level 1 (MICRO), type 2 (NEW_OPT) New opt (flag): -trk_opp_orient. Applies only to TRK format output. Will oppositize the voxel_order for the TRK file.
04 Jun 2019, RC Reynolds, plug_tag, level 2 (MINOR), type 4 (BUG_FIX) use calloc to init last 4 bytes of tag string in thd_dsetatr.c This was leaving garbage in HEAD file. Thanks to A Nugent for noting the problem. 04 Jun 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -dset_extension, -storage_mode
03 Jun 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) allow ricor processing in case of multi-echo data Done for K Dembny.
30 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 5 (MODIFY) apply full Gaussian for blur, rather than truncated Truncated is okay, but has cubical extents, rather than spherical.
29 May 2019, DR Glen, @auto_tlrc, level 2 (MINOR), type 5 (MODIFY) auto_tlrc changes NIFTI in and out fixes, prefix option, 3dAllineate option Default interpolation changes, one pass combination default too
24 May 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) 4+1 new features 1) Default threshold is now 0 2) Default threshold scale is now 0-10 instead of 0-1 3) Default max threshold scale exponent is now 5 instead of 4 4) Default colorscale is now Reds_and_Blues_Inv PLUS 5) User can set AFNI_AUTORANGE_PERC to have the autoRange computed as percentile point (from 2-99) of the nonzero absolute values in the OLay brick. However, this doesn't work with warp-on-demand datasets now, so it is confusing. Therefore, the default setting of this is 0, which leaves the autoRange to be the maximum absolute value.
23 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add options -regress_anaticor_full_gaussian, -regress_anaticor_term_frac Also, save fanaticor_mask_coverage dataset. 23 May 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Would not run in python2, because of subprocess.run() call (only py3). Now updated to using afni_base.py functions to execute shell cmds.
22 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) blurs are now truncated Gaussians by default, making them flat 22 May 2019, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 0 (GENERAL) start with 'MAKE ?= make', and use MAKE exclusively Thanks to J Bacon for the suggestion. 22 May 2019, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Somewhat big changes: warns block updated and radcor block added. Left-right flip and @radial_correlate checks now in; other tweaks. 22 May 2019, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL) Improved help file (lists blocks, line to online help). Better formatting of a couple things; warn level coloring added. 22 May 2019, P Taylor, @djunct_json_value.py, level 2 (MINOR), type 1 (NEW_PROG) Tiny program to extract values from JSONs. Just used by apqc_make_tcsh.py.
20 May 2019, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 4 (BUG_FIX) modify pane_scale to match updates for AFNI_PBAR_FULLRANGE
17 May 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 6 (ENHANCE) Also add 'AFNI Forum' and 'Prog Helps' buttons 17 May 2019, RW Cox, AFNI GUI, level 1 (MICRO), type 6 (ENHANCE) Add 'AFNI News' button, above 'AFNI Tips'
16 May 2019, RC Reynolds, gen_ss_review_scripts, level 2 (MINOR), type 6 (ENHANCE) add uvars flip_check_dset and flip_guess Add 'flip guess' to review_basic output. 16 May 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) add read_text_dictionary, read_text_dict_list, convert_table2dict Also, allow table2dict in write_data_as_json. This allows for easy I/O of tables, and the ability to convert them to json form.
15 May 2019, RC Reynolds, gen_ss_review_scripts, level 2 (MINOR), type 6 (ENHANCE) add uvar have_radcor_dirs 15 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 6 (ENHANCE) modify output file names to handle special cases of all_runs and errts
14 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add options -radial_correlate_blocks and -radial_correlate_opts Run @raidal_correlate at the end of each specified block, creating one correlation volume per run. Each voxel gets the correlation of its time series with a local (slighly Gaussian weighted) average. 14 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL) Change some fields in pbar json, for greater utility. Also make new default ftype for output cbar (jpg). 14 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) More pbar control: put in afni's '-XXXnpane P' behavior. Same option name used in this prog.
13 May 2019, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL) fail if using MIN_OUTLIER, but not enough time points Thanks to H Mandelkow for noting this. 13 May 2019, P Taylor, @DriveSuma, level 1 (MICRO), type 0 (GENERAL) Some help output has non-UTF8 chars in it; default help now *won't*. 'MICRO' might be too strong a designation for this change... 13 May 2019, P Taylor, 3dRprogDemo.R, level 1 (MICRO), type 0 (GENERAL) Some help output has non-UTF8 chars in it; default help now *won't*. 'MICRO' might be too strong a designation for this change... 13 May 2019, DR Glen, 3dExchange, level 2 (MINOR), type 1 (NEW_PROG) Exchange specified values in a dataset Takes two columns of numbers to map input to output
10 May 2019, RC Reynolds, NIFTI, level 1 (MICRO), type 6 (ENHANCE) add NIFTI_ECODE_QUANTIPHYSE 10 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Allow for comments about pbar ranges to be stored when saving pbar. Also, the pbar text info will now be stored in dict/JSON-able form.
09 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 2 (NEW_OPT) replace 3dLocalstat with 3dmerge for locally ~averaged time series One can choose between the methods, but 3dmerge is much faster. Included options are -use_3dmerge, -corr_mask and -merge_nrad, as well as -do_clean and -verb. 09 May 2019, RC Reynolds, 3dTcorrelate, level 1 (MICRO), type 6 (ENHANCE) include old history of xset
08 May 2019, RW Cox, 3dQwarp, level 1 (MICRO), type 5 (MODIFY) Expand (somewhat) max displacement of component warps 08 May 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) allow AFNI_BLUR_FIRFAC to get near zero This can be abused for a 'fast ANATICOR', for example. Since sigma = 0.4246609 * fwhm, consider using: sfac = 1/(2*.0.4246609) = 1.17741 That number of sigmas should match the half width at half max, which should terminate the blur just after a half height. Or use 2*FWHM and sfac = 1.17741/2 = 0.588705 to make it more flat, with a min contribution of ~0.84, rather than 0.5, yet limiting the output to the same HWHM radius (e.g. FWHM=80mm with sfac=0.589 results in a fairly flat blur out to a radius of ~20 mm). 08 May 2019, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) add -module_dir
07 May 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -timing_to_1D_warn_ok to make some conversion issues non-fatal Done for J Wiggins and M Liuzzi. 07 May 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE) add deg2chordlen() to return distance traveled due to a rotation
06 May 2019, RW Cox, Clusterize, level 1 (MICRO), type 6 (ENHANCE) Add 'ICent' (Internal Center) to coordinate option In addition to Peak and Cmass. The problem with Peak is that it can be way off on an edge. The problem with Cmass is that it can be outside the actual cluster. ICent is sort of like Cmass but will be inside the cluster.
01 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Allow -set_subbricks to take string labels for subbricks as usable args. Excellent idea, Rasmus! 01 May 2019, P Taylor, @djunct_is_label.py, level 1 (MICRO), type 0 (GENERAL) Tiny program to see if input is an integer (-> index) or str (-> label). Just used by @chauffeur_afni for -set_subbricks reading.
29 Apr 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Keystrokes for cluster jumpingn jumps to the next cluster's peak/cmass N jumps to the previous cluster's peak/cmass If focus is NOT in a cluster, then goes to the nearest cluster in space instead. [For John Butman, NIH/CC - happy NOW?]
25 Apr 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) -regress_bandpass now takes any positive number of frequencies pairs Done to appease the mighty P Taylor.
24 Apr 2019, RW Cox, 3dPVmap, level 1 (MICRO), type 6 (ENHANCE) Two changes 1) Add singular value fractional variance-explained output 2) Change fixed cubic detrending to polort=N/50 detrending
23 Apr 2019, RC Reynolds, 3dAllineate, level 1 (MICRO), type 6 (ENHANCE) Allow '^' to denote a power in -autoweight, in addition to '**' This is to avoid protecting the string in quotes, making it easy to pass from afni_proc.py to align_epi_anat.py to 3dAllineate.
22 Apr 2019, RW Cox, 1dApar2mat, level 1 (MICRO), type 1 (NEW_PROG) Compute the affine matrix from the parameters from 3dAllineate 22 Apr 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -tsv_labels This can be used to specify column labels to be used for onset time, duration, trial type, and optional modulators.
19 Apr 2019, P Taylor, @Spharm.examples, level 2 (MINOR), type 0 (GENERAL) Just updated paths/names: tarball getting used no longer exists. No change in functionality (j'espere).
18 Apr 2019, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT) Include -deoblique and -giant_move opts. For oblique data, and/or heavily rotated, shifted, etc. 18 Apr 2019, DR Glen, whereami GUI with wrong atlas, level 1 (MICRO), type 4 (BUG_FIX) whereami would crash afni GUI if atlas was not found Also more descriptive message when no available atlases
17 Apr 2019, DR Glen, whereami minimum space, level 1 (MICRO), type 5 (MODIFY) Should have at least the space of the dataset coordinate

auto-generated by afni_history on Oct 17 2019