AFNI HISTORY

level 2 and higher

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


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

---- log of AFNI updates (most recent first) ---- 03 Jun 2020, P Taylor, lib_mat2d_plot.py, level 3 (MAJOR), type 0 (GENERAL) Many updates to functioning, defaults, reading argv, applying user opts. Help file added as well; works with main proc: fat_mat2d_plot.py. 03 Jun 2020, P Taylor, fat_mat2d_plot.py, level 3 (MAJOR), type 1 (NEW_PROG) FINALLY, a python3 program to plot 3dTrackID and 3dNetCorr output. Plots *.grid and *.netcc files; replaces fat_mat_sel.py.
02 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add PM (plus/minus) curve plotting options Added to the 'Colors Etc' menu. Curves, Bars, and Fill.
01 Jun 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) in populate_nifti_image(), call time series only if ntt>1 or NVALS==1 This is to avoid confusion when a time series is used to master a non-time series dataset. 01 Jun 2020, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_regs and -show_regs_style Show column indices or labels of an xmat.1D file with empty (all-zero) regressors. An index list can be space or comma-separeated, or encoded. Example 30 shows typical use cases. Added for S Haller. 01 Jun 2020, P Taylor, lib_mat2d_base.py, level 2 (MINOR), type 0 (GENERAL) Migrated from lib_mat2d.py; tweaks added. Add in few more mat2d attributes; rearrange methods. 01 Jun 2020, P Taylor, lib_mat2d.py, level 2 (MINOR), type 0 (GENERAL) Start some new functionality for 2D matrices. In particular, these are for 3dTrackID and 3dNetCorr output. 01 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) For vstat with seedbased corr (rest), use 0.2 as thr value of corr map. The value 0.3 seemed pretty high (esp. if no smoothing is applied). 01 Jun 2020, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL) Add new funcs for convenient message printing, in the AFNI style. IP(), EP() and WP(), which are wrappers to use APRINT(). 01 Jun 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Reformat report*.1D tables a bit. Add in a KEY; change U/W to A/B; minor format stuff.
31 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Change range of grayscale when EPI is ulay (ve2a and LR flipcheck). Now 2-98percent (nonzero). 31 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX) Two bug fixes: 1) where src_prefix is defined. 2) Make sure labels/atlases of ATL|SEG followers are passed along.
30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 1 (NEW_PROG) Perform modal smoothing, and go back and add in any ROIs that were lost. May be useful in @animal_warper; may be good to add mask stuff, too. 30 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Default modal smoothing now is with replacement of any lost ROIs. Uses @djunct_modal* script; opt to not replace. More QC images now, too. 30 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) String selector of lost ROIs now is only comma-separated list. Discovered couldn't have both comma- and '..'-separated list in selector. 30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 0 (GENERAL) Now use *.nii.gz files for all intermeds, not *.nii. Works better with @animal_warper this way. 30 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Apply input_abbrev earlier in processing. Homogenize naming, I think, if it is being selected.
28 May 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Add curve smoothing plot to graph viewer Invoked from 'Colors Etc' menu, or by pressing the 's' key. [For GC] 28 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Now report DF information in vstat block. Needed to be able to interpret F-stat and t-stat values.
26 May 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Two major changes in output: ve2a and LR-flipcheck now have EPI as ulay. Most anats are SSed, so better edges? Thanks for suggestion, O Esteban! 26 May 2020, P Taylor, @djunct_edgy_align_check, level 3 (MAJOR), type 0 (GENERAL) Several changes to make this appropriate using EPI as ulay. New opts, couple small bug fixes, couple tweaks. 26 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Now output an AFNI-style string selector of 'lost' ROI values. This might make it easier to see the diffs the volumes.
25 May 2020, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE) add libexpat.1.dylib to EXTRA_INSTALL_FILES R was upgraded to 3.6 (on the 10.12 build machine), since that is the current G Chen version requirement, making R_io.so work for people with only 3.6. But libexpat was upgraded too, which afni depends on, meaning systems needed that new version of libexpat, or afni would not work. Instead, libexpat.1.dylib is now simply included with the binaries. Thanks to S Gotts and K Tran for reporting the problem.
22 May 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Change this prog to do all work in a workdir that can be cleaned. Should not have any effect on the usage or outputs.
21 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT) add options -NN1, -NN2 and -NN3 Also, fix tiny origin shift when large zero-padding is applied. 21 May 2020, P Taylor, afni_seeds_per_space.txt, level 3 (MAJOR), type 0 (GENERAL) Keep up with change of macaque standard space naming: stereoNMT -> NMT2. 'stereoNMT' is an ex-parrot. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 3 (MAJOR), type 1 (NEW_PROG) Adjunct program for @animal_warper.py; build ROI report table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Add reports of warped and unwarped ROIs, via adjunct_aw_tableize*.py. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL) Require mode_smooth_size as input, and include it in table. Thanks to D Glen and A Messinger for helpful feedback+inputs. 21 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Report now reports mode_smooth_size. Thanks to D Glen and A Messinger for helpful feedback+inputs.
20 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update THD_mask_erode_sym() akin to take NN param This matches the dglen update to THD_mask_dilate(). 20 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX) fix history and memory loss
19 May 2020, DR Glen, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) nzvolume - volume of nonzero voxels
18 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL) Large number of under-the-hood changes, as well as new opts. More general handling of followers and choosing file abbrevs. 18 May 2020, P Taylor, afni_seeds_per_space.txt, level 2 (MINOR), type 0 (GENERAL) Updated APQC seed locations for stereoNMT space. More centralized now in GM and in specific ROIs; aud away from vessel.
14 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Large number of under-the-hood changes, for readability/clarity. Change echo->printf, spacing, clear comments, etc. No output changes.
11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) update web links to help pages in uber*.py Update uber_align_test.py, uber_skel.py, uber_subj.py and uber_ttest.py. 11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) updates for python3 Update xmat_tool.py, quick.alpha.vals.py, read_matlab_files.py, uber_align_test.py and uber_skel.py.
04 May 2020, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 6 (ENHANCE) make partual updates for python3 04 May 2020, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY) remove tabs from a bunch of files 04 May 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX) fix download of test file Thanks to Gerome on MB for reporting the problem. 04 May 2020, P Taylor, @Install_IBT_DATASETS, level 2 (MINOR), type 1 (NEW_PROG) Installer for the Indian Brain Templates. Enjoy.
30 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 0 (GENERAL) Added YouTube button to afni GUI.
29 Apr 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY) for recur, def to pub/dist/bin/misc; terminate on failed test download 29 Apr 2020, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 6 (ENHANCE) add AFNI_DRIVE_OPTS_XVFB env var for adding opts to Xvfb This will probably be modified later, but it allows one to pass something like '-nolisten inet6' if IPv6 is not working. Thanks to W-L Tseng.
27 Apr 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Added a help example for integrating output into afni_proc.py. ... because otherwise *I* forget how to use the outputs.
24 Apr 2020, P Taylor, 3dLMEr, level 2 (MINOR), type 0 (GENERAL) Updating this R file for GC. So I don't really know what the changes do. ... though I reeeallly want to pretend the changes were mine, ALL MINE. 24 Apr 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL) Sidedness of testing will no longer be checked for non-stat thr vols. It must be Daniel Glen's birthday today (two-sided, non-stat p<0.9999).
23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Added new help example. Demonstrates useful colorbar-entry functionality. 23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Use '-colorscale_idx_file ..' to control AFNI env var AFNI_COLORSCALE_xx. Provides a way for user-created cbar info to be input+used.
21 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 2 (NEW_OPT) Added -all_dsets to load all datasets togther.
14 Apr 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) if dataset inputs had full paths, use them in proc script Thanks to W-L Tseng for pointing out the discrepancy.
10 Apr 2020, RW Cox, AFNI gui, level 2 (MINOR), type 2 (NEW_OPT) Add -norm option for normal font sizes
08 Apr 2020, RW Cox, 1dplot, level 2 (MINOR), type 6 (ENHANCE) Add '0' to the -dashed option -dashed codes are now 1 = solid 2 = longer dashes 3 = shorter dashes 0 = no line, use boxes Code 0 is new, to allow a graph with some data plotted with lines and some without.
07 Apr 2020, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) add -see_also and -ver_man to help create a quick man page To create a man page (via help2man), consider: nifti_tool -see_also > nt.see_also.txt help2man --help-option=-help --version-option=-ver_man \ --include nt.see_also.txt --no-info nifti_tool \ | gzip > nifti_tool_manpage.1.gz after which one can install the file, or test via man ./nifti_tool_manpage.1.gz (see the uncompressed version for syntax).
31 Mar 2020, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 6 (ENHANCE) update for python3 31 Mar 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX) fix lib_system_check:self.os_dist for newer python
30 Mar 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) have module_test_lib.py (and so afni_proc.py) work on python 2.6 again Done for S Horovitz. 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) rigid_equiv - rigid equivalent affine alignment 30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX) NIFTI view equivalent for epi2anat alignment fix
27 Mar 2020, DR Glen, @animal_warper center_shift, level 2 (MINOR), type 2 (NEW_OPT) Allow for center shifting or not
24 Mar 2020, RC Reynolds, python_module_test.py, level 2 (MINOR), type 5 (MODIFY) restore approximate previous behavior
23 Mar 2020, RC Reynolds, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) add options -oblique_recenter and -oblique_recenter_raw Adjust the origin so the cardinalized 0,0,0 (e.g. seen in the afni GUI) is in the same brain location as it was originally (in the scanner?). So when viewing an oblique volume on top of a '3dWarp -deoblique' output, coordinate 0,0,0 will match between them.
20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs 20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY) fix PY_DIR, update PY vars, add list_py_libs
19 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) fix use of module_test_lib.py with change to new afnipy dir
17 Mar 2020, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT) Modify font size options - hopefully easier now 1) Change meaning of 'plus' fonts to be bigger than before. 2) Change so that 'plus' twice on command line equals 'big'. 3) Add simpler options '-big' and '-plus' and '-minus'. Combined, these should make it easier to do font size changes.
12 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) point web help for program to sphinx tree Also, added -hweb/-h_web for python progs that use option_list.py. 12 Mar 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 2 (MINOR), type 1 (NEW_PROG) test for a valid DrawingAreaWidgetClass pointer 12 Mar 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) This program has been deemed unnecessary. Thanks for the FS folks for discussions/clarifications on this. 12 Mar 2020, P Taylor, 3dReHo, level 2 (MINOR), type 0 (GENERAL) Alter output format if ROI neighborhood values of ReHo are calc'ed. Make 2 col (ROI val; ReHo val). Output multiple text files, if nec, too.
11 Mar 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Swap ulay/olay in va2t (anat->ulay); clearer image, maybe. Make template (if used) ulay in most other QC blocks.
10 Mar 2020, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE) Add dataset-level weights to 3dttest++ Per the request of users in Tulsa. New options -setweight[AB] allow user to provide weights for the importance of a user in the calculations.
05 Mar 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY) for now, use mris_convert/3dcopy for extra annot files So standard mesh version will not have a proper label table, but the values will be appropriate and more usable in suma. This is done to import the Schaefer/Yeo atlases onto standard meshes. Done with D Glen.
27 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -fsannot_ver; apply -extra_annot_labels output as -extra_fs_dsets 27 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) New opt '-warpscale' added; is a new opt in 3dQwarp, can be tweaked here now. Control flexibility of warps. Right now testing different values.
26 Feb 2020, RW Cox, machdep, level 2 (MINOR), type 6 (ENHANCE) First step for allowing floating round randomization Code in machdep.c, enabled by environment variable AFNI_RANDOMIZE_ROUNDING, lets a program invoke macro RAND_ROUND to randomize the IEEE rounding mode. This requires compiling with the flag -DUSE_FENV to enable use of the C99 function fesetround() to set the rounding mode -- see machdep.h. So far, only 3dAllineate has any parts that use RAND_ROUND -- that is, if you set AFNI_RANDOMIZE_ROUNDING to YES and run 3dAllineate, the results will change from a 'normal' run. How much? That's the point of this update, to see how sensitive the output is to the accumulation of tiny changes. 26 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Crashing in cases of 'pythonic' APQC with no censoring. Have fixed now. 26 Feb 2020, DR Glen, @animal_warper ROIdset followers, modal smoothing, level 2 (MINOR), type 2 (NEW_OPT) Allow for ROIs to follow into template space and modal smoothing ROIs are transformed with nearest neighbor interpolation Both ROIs and segmentation followers from the template space are now modally smoothed within 3 voxel neighborhoods
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL) New min|max range on vox size; update report text. Based on tests with FS data. 25 Feb 2020, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX) Minor bug fix, caught by RCR. Or was it first *added* by RCR???? ... Nope. It was added by me. Sigh.
24 Feb 2020, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add -warpscale option To scale the warp displacments down at each level, for experimentation.
22 Feb 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Temporary files now have a random string in their prefix. Thus, can have multiple runs in same directory simultaneously sans problem e. 22 Feb 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can control AGIF frame rate, using opt (-agif_delay) to control AFNI env var. Thanks to RCR for pointing out the env var.
21 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Crashing in cases of 'basic' APQC with no outlier-based censoring. Have fixed now.
19 Feb 2020, RC Reynolds, afni_python_wrapper.py, level 3 (MAJOR), type 1 (NEW_PROG) replaces afni_util.py as a main This program can theortically be used to call any AFNI python function from the shell. 19 Feb 2020, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY) no longer available as a main executable 19 Feb 2020, P Taylor, adjunct_select_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_select_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_make_script_and_rst.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_is_label.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_is_label.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_combine_str.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, adjunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @djunct_calc_mont_dims.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, DoPerRoi.py, level 2 (MINOR), type 0 (GENERAL) Renamed from @DoPerRoi.py. Purge @ symbol in Python progs, for purpose of repackaging/distribution. 19 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL) New QC image outputs added. One for skullstripping (orig space) and one for warping (ref space).
18 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) help examples now include some developed outside of afni_proc.py This includes some class demos, along with pamenc and NARPS. Include a line about whether each example is reasonably recommended. Done to appease the mighty P Taylor.
17 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Reorganized under the hood, deal with censoring in a better way. Easier to tweak/update changes now. 17 Feb 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Opt -censor_hline can now take a keyword NONE as an entry. Useful if looking at multiple inputs and only some have censor lines.
14 Feb 2020, RW Cox, afni GUI, level 2 (MINOR), type 4 (BUG_FIX) Get Atlas Colors working again Problem: 2 generations of overlay colorization changes. a) Overlay went from indexes to RGB b) Overlay went from indexes or RGB to RGBA The atlas overlaying function didn't allow for these very well, especially the latter. Obviously, this can't be my fault since I'm the boss - even though I wrote the offending code. Someone must have joggled my brain. 14 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -compare_opts_vs_opts One can compare two afni_proc.py commmands sequentially, that are not part of the stored examples list. Consider: afni_proc.py ... first option set ... \ -compare_opts_vs_opts \ ... second option set ... It is okay for 'second option set' to include the afni_proc.py command name, in case two scripts are concatenated. 14 Feb 2020, DR Glen, @animal_warper dset followers, level 2 (MINOR), type 2 (NEW_OPT) -dset_followers to apply same transformations as dset 14 Feb 2020, DR Glen, @Align_Centers shift xform, level 2 (MINOR), type 2 (NEW_OPT) Move center/origin by known amount from 1D file Large translations in nonlinear warp interpolation can use vast amounts or memory in the 3dNwarpApply implementation. By doing center alignment separately, we can remove the memory and computational costs. The new options are -shift_xform and -shift_xform_inv.
12 Feb 2020, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) add ability to compare against examples Add options -compare_opts, -compare_example_pair, -show_example and -show_example_names. Consider these examples: afni_proc.py -show_example 'Example 11b' afni_proc.py -show_example_names afni_proc.py ... my options here ... -compare_opts 'Example 11' Motivated by C Gaillard and P Taylor. 12 Feb 2020, DR Glen, 3dCM Icent, Dcent, level 2 (MINOR), type 2 (NEW_OPT) alternative centers To force centers to lie within a region -Icent for internal center, -Dcent for distance center
07 Feb 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) reduce X11 program deps Possibly define LLIBS_X11 in top-level Makefile (as current LLIBS) and then remove X libs from LLIBS. M.INCLUDE will define LLIBS if not set. Move suma_help to IMOBJS. 07 Feb 2020, RC Reynolds, Makefile.linux_fedora_28_shared, level 2 (MINOR), type 6 (ENHANCE) build main non-X11, non-SUMA AFNI program without X deps Set LLIBS_X11 to current LLIBS, and give it to SUMA_LINK_LIB. Remove all X11 libs from LLIBS. Add -DREPLACE_XT to CEXTRA. Note: without REPLACE_XT, LLIBS could still just use Xt and X11. And made the same mods to Makefile.linux_xorg7_64.
05 Feb 2020, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT) Add -LJorder option To order voxels by their Ljung-Box statistics. 05 Feb 2020, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT) list all global options via 'PROG.py -optlist_show_global_opts' Also, add -optlist_show_argv_array to display afni_proc.py options in python dictionary format. This could be done with any OptionList-based python program. 05 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add inital new library for processing example, lib_ap_examples.py
03 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -extra_annot_labels 03 Feb 2020, P Taylor, @djunct_anonymize, level 2 (MINOR), type 1 (NEW_PROG) Anonymize files, and maybe add a note. Can either edit input directly, or make a copy + edit that. 03 Feb 2020, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT) Can anonymize output dsets: -anonymize_output. Fairly self-explanatory opt.
02 Feb 2020, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT) Add -qval option to 3dPVAL [for GC]. Merry Groundhog Day!
29 Jan 2020, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX) Couldn't deal with volumes that had RGB type, which happens for DEC maps. Has been fixed now. 29 Jan 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX) The input opt '-xfile ..' was broken; now it is fixed. Fix class inits, as well, under the hood.
27 Jan 2020, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE) add basis=BASIS parameter when defining timing class Done for geenaianni on MB. 27 Jan 2020, RC Reynolds, @diff.tree, level 2 (MINOR), type 2 (NEW_OPT) add -show_list_comp, to do pairwise comparison of file names 27 Jan 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE) gzip SUMA/*.nii, except for SurfVol 27 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) Program now outputs QC images automatically. These are output into a PREFIX_QC directory each run. 27 Jan 2020, P Taylor, @SSwarper, level 3 (MAJOR), type 0 (GENERAL) Large set of updates; many new opts added, too; generally much improved warps. Heavily tested on 178 subj across studies; output fnames are same, though. 27 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Fixed bug in QC. Broke when there was one stim used (bad scalar -> list conv).
26 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program now requires specifying a mode for re/defacing. One can also output all types of re/defacing simultaneously.
24 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL) This program has been revamped and updated, including having a new ref vol. Syntax for running this has totally changed (options exist). 24 Jan 2020, P Taylor, @afni_refacer_make_master_addendum, level 3 (MAJOR), type 0 (GENERAL) This program just records additional tweaks to refacer ref vol. Not really meant to be run on its own; for future reference only.
23 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 4 (ROIs and mask==1 data) Done for J Gonzalez-Castillo.
22 Jan 2020, RW Cox, 3dREMLfit, level 3 (MAJOR), type 6 (ENHANCE) Compute Ljung-Box statistic for -Rvar dataset. Provides a measure of how temporally correlated each voxel's pre-whitened residuals are. Small LB value = good fit by the ARMA(1,1) model. Sub-brick is coded as a chi-squared statistic for use in thresholding in the AFNI GUI. 22 Jan 2020, RC Reynolds, plug_realtime, level 3 (MAJOR), type 0 (GENERAL) add ROIs and data mask method Added corresponding demo: AFNI_data6/realtime.demos/demo_3_ROIs_n_data 22 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE) add handling of magic version 3 (all data light)
21 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Increase thresholds and cbar range in vstat_seedcorr and regr_corr dsets. Clearer QC, methinks, based on several different group dsets.
17 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) New pieces of QC: corr brain image in regr block. Shows corr of mean residual with everything. Have a nice day.
15 Jan 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) corr_* dsets are now correlations with ROI averages They were previously average correlations with each ROI voxel. The new maps look similar, but are probably more natural and have nicer scales. Requested by P Taylor.
14 Jan 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL) Change text of animal_outs.txt. Add in a couple new dsets to be listed.
13 Jan 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add some make lists ; see 'make list_lists' 13 Jan 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) New pieces of QC: first, seedbased corr maps for non-task data. Second, censor-based warnings (general and per-stim). 13 Jan 2020, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) New function to read in seed list text file. Returns list of seed objs for APQC. 13 Jan 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Couple new options. Can specify colorbar and center coords now.
31 Dec 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY) Do not require out_limit. Currently will still show in driver. Done for P Taylor.
27 Dec 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 2 (NEW_OPT) New option(s) to not just *check* a dset for FS-ability, but to correct it. The '-fix_all' and accompanying options control this. Bonne idee, DRG!
26 Dec 2019, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX) Fix one of the test criteria (-is_mat_even). Thanks, S. Torrisi, for pointing this out.
25 Dec 2019, DR Glen, erosion/dilation neighborhoods, level 2 (MINOR), type 5 (MODIFY) Allow for NN1,NN2,NN3 neighborhoods for erosion and dilation 3dAutomask and other programs use these functions the depth option in 3dAutomask gives a depth of automask NN1,2,3
17 Dec 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) allow labels as column selectors when reading xmat.1D files Done for G Chen.
12 Dec 2019, RW Cox, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Add -zcensor option Remove from consideration any time point t where xset(t) OR yset(t) is identically zero (in the mask). For Peter Molfese and Emily Finn. Merry X! 12 Dec 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY) More centers - find deepest near voxel closest to Center of Mass Came from CodeConvergence idea by Meghan Robinson Voxel closest to center of mass is similar to latest ICent in Clusterize GUI
10 Dec 2019, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV) Add 'Zoom lock' to the locking capability Also a new environment variable AFNI_ZOOM_LOCK to turn this on at startup, vs interactively later. 10 Dec 2019, RC Reynolds, uber_proc.py, level 2 (MINOR), type 5 (MODIFY) separate into main/lib/gui, so one can run -help w/out PyQt4
09 Dec 2019, RC Reynolds, 3dTagalign, level 2 (MINOR), type 2 (NEW_OPT) add -tagset Coded by T Holroyd.
29 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -volreg_opts_ewarp, to pass additional volreg EPI warp options Added for L Fernandino.
26 Nov 2019, RW Cox, @afni_refacer_run, level 3 (MAJOR), type 6 (ENHANCE) Modify shell dataset to avoid some brain clipping Mostly by eroding the inside of the brain shell. Also a couple little tweaks to the script.
21 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) update babble about FreeSurfer in help 21 Nov 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 4 (BUG_FIX) add 'endif' for if( $warpdrive_method == '3dWarpDrive' Thanks to T Holroyd for reporting and fixing this. 21 Nov 2019, RC Reynolds, 3dRank, level 2 (MINOR), type 4 (BUG_FIX) fix storage_mode handling (re-allow niml.dset output) Thanks to dmoracze on the Message Board for noting the problem.
19 Nov 2019, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) add -fs_setup, to optionally source $FREESURFER_HOME/SetUpFreeSurfer.csh
14 Nov 2019, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 0 (GENERAL) New output: fs_ap* dsets for tissue-based reg in afni_proc.py;. New output: *REN_gmrois* dsets for tracking/corr mats in FATCAT. 14 Nov 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-make_rank_dsets ..', bc *rank* dsets no longer make by def. The *REN* dsets should be used instead; opt just for back compatability.
13 Nov 2019, DR Glen, AFNI Clusterize, level 2 (MINOR), type 4 (BUG_FIX) ICent error Couple bugs in ICent location computation - thx to Meghan Robinson
12 Nov 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY) Center for deepest voxel closest to Center of Mass Made in CodeConvergence with Chris Rorden and Meghan Robinson
11 Nov 2019, DR Glen, @suma_acknowledge, level 2 (MINOR), type 1 (NEW_PROG) Make simple graphs of collaborations and classes Made for AFNI bootcamps using SUMA graph datasets This may be useful for acknowledgement for general use
01 Nov 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) process out.mask_at_corr.txt, the anat/template Dice coefficient Requested by P Hamilton. 01 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) create out.mask_at_corr.txt, the anat/template Dice coefficient Requested by P Hamilton.
25 Oct 2019, RW Cox, afni GUI driver, level 2 (MINOR), type 6 (ENHANCE) butpress commands to image viewer butpress=Colr or Swap or Norm to simulate button presses For Paul. 25 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) allow selectors on -dset* options (cannot mix with removal options) Requested by E Finn.
24 Oct 2019, RW Cox, AFNI gui, level 2 (MINOR), type 3 (NEW_ENV) AFNI_IMAGE_COLORSCALE defines colorbar for image viewer window Formerly fixed, now user can specify the color scale to use here from one of these: magma viridis plasma googleturbo Also, I restored the 'g' (gamma) button affect on this color scale. 24 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add combine methods m_tedana, m_tedana_OC Can run tedana from MEICA group: https://github.com/ME-ICA/tedana https://tedana.readthedocs.io
23 Oct 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 1 (NEW_PROG) Script to check properties of a dset, see if suitable for FS's recon-all. The check criteria have been built over time, empirically.
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
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
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.
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 .
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
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, 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.
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.
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.
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.
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, 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, 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, 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
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, 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.
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.
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, 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)
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.
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
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.
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.
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.
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).
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.
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, 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.
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.
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.
19 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) add surf_vol uvar
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.
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.
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, 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
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, 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, 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.
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).
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
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!
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.
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.
16 Apr 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX) verify av_space == +tlrc before setting template Thanks to P Molfese and P Taylor for noting the problem. 16 Apr 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) if do_apearch, update .bashrc to source all_progs.COMP.bash Done to appease the mighty P Taylor.
15 Apr 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE) Make -bysub option work with directory names A command like afni -bysub ~/data/UCLA_pamenc20 will find all 'sub-*' subdirectories in the given directory, and process those individually via the older '-bysub' operation. This makes it simple to read in an entire BIDS hierarchy. Note that the recursive descent for each 'sub-XXX' name will include derivatives (if found).
12 Apr 2019, DR Glen, unWarpEPI.py python3, level 2 (MINOR), type 5 (MODIFY) unWarpEPI.py python3 compatible 12 Apr 2019, DR Glen, unWarpEPI.py python3, level 2 (MINOR), type 5 (MODIFY) unWarpEPI.py python3 compatible
11 Apr 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) add functions gaussian_at_fwhm, gaussian_at_hwhm_frac 11 Apr 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -combine_tedort_reject_midk It might be a good idea to set this to 'no', so less gets rejected. 11 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) Brainnetome atlas This atlas is now included in the standard distribution This also is in the default list of atlases
08 Apr 2019, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 2 (NEW_OPT) add options -reject_midk and -reject_ignored It seems likely that '-reject_midk 0' should be the default.
07 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) Eickhoff-Zilles 2.2 MPM atlas This atlas is the newer 2.2 version of the MPM atlas This atlas replaced the 1.8 version in the list, but both are kept in the binary distribution
05 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV) HCP Glasser atlas in AFNI atlases Mike Beauchamp and Meghan Robinson contributed atlas Now included and first in default list too This atlas is in MNI space (not in its original Contee grayordinate surface space. Additionally, all the pmaps (probability maps) have been removed from the standard distribution and default list
20 Mar 2019, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 4 (BUG_FIX) sync crorden/dcm2niix_console with repo, version v1.0.20181125 This is possibly to correct a bug with -m and partial brain coverage.
15 Mar 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) include tr field in uvars, and report it as TR in basic 15 Mar 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Better behavioring of -box_focux_slices when ulay and refbox grids differ. Now checking grid similarity and resampling refbox if needbe.
14 Mar 2019, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE) add gifti/regress_tests tree This was also added to https://github.com/NIFTI-Imaging/gifti_clib repo.
10 Mar 2019, RW Cox, 3dXClustSim (ETAC), level 2 (MINOR), type 0 (GENERAL) Sort FOM results to cast out duplicates from same iteration Should make Global ETAC slightly less conservative.
08 Mar 2019, RW Cox, InstaCorr, level 2 (MINOR), type 4 (BUG_FIX) Bandpass error found by the wandering Spaniard Problem: very long time series (over 2000) analyzed *without* Bandpass would give error message and then give useless results. Solution: if Bandpass is turned off, that is signaled by setting the upper freq cutoff to a large value. Then the FFT cutoff index is computed from that as jtop = ftop/df where df = 1/N*dt, so we have jtop = ftop*N/dt. For large N and large ftop, this is integer overflow. Therefore, compute jtop in float, not int, then check it first. D'oh.
07 Mar 2019, RC Reynolds, gen_ss_review_table.py, level 3 (MAJOR), type 2 (NEW_OPT) add -report_outliers and support options Add -report_outliers_{fill,header}_style, -write_outlier, and -outlier_sep for controlling the table presentation. Will use -write_table instead of -tablefile going forward.
06 Mar 2019, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE) if VR mismatch warning, specify whether AFNI uses the field Done for B Benson.
05 Mar 2019, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE) show subject counts; change line len and ddirs; no require on restricted
28 Feb 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX) mask dset must include extension
27 Feb 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Include grayplots in the APQC HTML file. Should add some extra info about residuals/modeling/the meaning of life. 27 Feb 2019, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Put a try/except at start, to set MPLBACKEND env if running w/o DISPLAY. Useful for current settings on Biowulf (and possibly elsewhere).
26 Feb 2019, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) add -dset_sid_list, -hpad, -tpad Add -dset_sid_list to specify subject IDs explicitly. Also, add -hpad/-tpad; less indentation for 3dttest++.
25 Feb 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE) add modulators to -multi_timing_to_event_list output Done for D Jangraw. 25 Feb 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) try to get mask_dset from TSNR output
22 Feb 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE) handle shells with paths in get_current/login_shell() 22 Feb 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -tlrc_NL_force_view, to handle sform_code=2 in auto_warp.py result Done for I Berteletti.
19 Feb 2019, P Taylor, apqc_make_tcsh.py, level 5 (SUPERDUPER), type 0 (GENERAL) Much functionality changed/improved (hopefully). More output, better formats, help and HTML framework. 19 Feb 2019, P Taylor, apqc_make_html.py, level 5 (SUPERDUPER), type 0 (GENERAL) Much functionality changed/improved (hopefully). More output, better formats, help and HTML framework. 19 Feb 2019, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Line thickness of plots now adjusts with number of points. Useful as the number of time points increases (hopefully).
11 Feb 2019, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) ... and can also turn off initial skullstripping and/or anisosmoothing. Options cleverly named: -skullstrip_off and -aniso_off. 11 Feb 2019, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Can turn off initial unifizing with -unifize_off. Useful if unifizing has been done to dset before using this cmd.
07 Feb 2019, RC Reynolds, demoExpt.py, level 2 (MINOR), type 1 (NEW_PROG) will now actually distribute Vinai's demoExpt.py and afniInterfaceRT
05 Feb 2019, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY) -infile_list now implies -no_wait 05 Feb 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX) allow -extent to vary across datasets 05 Feb 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Had been missing an endif. Now new and improved-- with endif!
30 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -volreg_post_vr_allin and -volreg_pvra_base_index These are to run 3dvolreg (or 3dAllineate) to a base within each run, before concatenating a transformation from each per-run base to the global EPI registration base. 30 Jan 2019, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT) Added '-montgap' and '-montcolor', for montage functionality. Users can now control montage borders (i.e., gaps) and color. 30 Jan 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Added '-montgap' and '-montcolor', for montage functionality. Users can now control montage borders (i.e., gaps) and color.
28 Jan 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) updates to make target, prog_list - grep out CMakeLists.txt - add some ptaylor python scripts - define and add DISCO_SCRIPTS 28 Jan 2019, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) add -help to @djunct_*.py 28 Jan 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Well, new functionality to existing opt: make focus box from ulay or olay. Keywords AMASK_FOCUS{O,U}LAY can be given to -box_focus_slices.
25 Jan 2019, P Taylor, @djunct_slice_space, level 2 (MINOR), type 4 (BUG_FIX) Couldn't deal with volumes that had subbrick selectors from @chauffeur*. Has been fixed now. 25 Jan 2019, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX) Couldn't deal with volumes that had subbrick selectors from @chauffeur*. Has been fixed now.
22 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_est_blur_detrend We might change the default to no detrending here. 22 Jan 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) add -show_obsoletes[_grep] and -show_system_progs Inspired by Z Saad.
19 Jan 2019, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX) Program wouldn't run with '-odir ..' opt. Now it will.
18 Jan 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) process df_info, and hand off new uvars 18 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) run 1d_tool.py -show_df_info, unless -regress_show_df_info no
17 Jan 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -show_df_info, to partition degrees of freedom in X-matrix
16 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) -regress_mot_as_ort now defaults to yes; use vr_base_external This should not affect results, it is prep for other evil designs.
08 Jan 2019, RW Cox, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Add '-nolite' option For backwards compatibility and testing. 08 Jan 2019, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY) -lite is now the default -- for speed Based on using @SSwarper with and without -nolite on 31 datasets. Results are very similar, and no systematic differences between the -lite and -nolite groups observed in mean or stdev. 08 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add -volreg_method, and corresponding options This allows one to use 3dAllineate for EPI motion registration. Options -volreg_allin_cost and -volreg_allin_auto_stuff (as well as the old -volreg_opts_vr) can be used to control -cost and other options.
04 Jan 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 5 (MODIFY) add -mod_hdr2, specific to NIFTI-2 headers 04 Jan 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) add regression testing scripts
03 Jan 2019, RW Cox, @afni_refacer_XXX, level 2 (MINOR), type 1 (NEW_PROG) Scripts to re-face a T1-weighted dataset @afni_refacer_make_master = makes the 'shell' dataset used to replace the face @afni_refacer_run = runs re-facing on one input dataset 03 Jan 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 5 (MODIFY) have -mod_hdr/-swap_as_nifti fail on valid NIFTI-2 header Re-allow processing of ASCII headers (via NIFTI-2). Also, incorporate updates from H Johnson.
26 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) incorporate more updates from the NIFTI_Imaging/nifti_clib repo
21 Dec 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX) Adjusted coordinator for a couple situations. Should be more centered for both 3D and 4D applications.
20 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) incorporate updates from the NIFTI_Imaging/nifti_clib repo And update Makefile.INCLUDE.
19 Dec 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) show execution syntax in both tcsh and bash Done to appease the mighty P Taylor. 19 Dec 2018, P Taylor, @djunct_montage_coordinator, level 3 (MAJOR), type 4 (BUG_FIX) This montage coordinator was noooot picking the right vol to focus on. That should be fixed via magical incantations now.
14 Dec 2018, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) include mask and params in -csim_show_clustsize
13 Dec 2018, RC Reynolds, @strip.whitespace, level 2 (MINOR), type 1 (NEW_PROG) stored under scripts_src; guess what it does
11 Dec 2018, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX) use mkdir -p; reconcile write_as_nifti and NIFTI prefix Thanks to C Smith for noting the issue.
10 Dec 2018, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) -cubic12 = use 12 parameter cubics instead of 24 Faster, and probably just as accurate.
05 Dec 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Have removed numpy dependency. Now, default afni_proc.py will output APQC HTML without numpy on comp. 05 Dec 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 0 (GENERAL) Have removed numpy dependency. Lighter installation/usage dependencies. 05 Dec 2018, P Taylor, @djunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL) Have removed numpy dependency. Lighter installation/usage dependencies. 05 Dec 2018, P Taylor, @djunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL) Have removed numpy dependency. Lighter installation/usage dependencies. 05 Dec 2018, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL) Have removed numpy dependency. Lighter installation/usage dependencies.
04 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) Makefiles: working towards using libmri.so Pass MRI_SHARED, and apply with SUMA_SHARED_LOPTS in SUMA.
03 Dec 2018, RC Reynolds, test.afni.prog.help, level 2 (MINOR), type 1 (NEW_PROG) test running -help on AFNI programs This is a build tool, not for the distribution.
02 Dec 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX) Will work with resting state analyses now. Fixed minor issue when no stat dset (just NO_STATS str) was present.
28 Nov 2018, RW Cox, 3dAllineate, level 2 (MINOR), type 6 (ENHANCE) Add lpa+ cost functional Like lpc+, with extra stuff added in for robustness. Per the suggestion of Daniel Glen, the master of allineation and punulation. 28 Nov 2018, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX) In py3, having a censor line caused graphing issues. Those issues have been resolved.
27 Nov 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL) Now make enorm and outlier plots even if no censor_dsets are in uvars. Also, on a more fun note, output censor frac below mot/outlier plots. 27 Nov 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL) Make python3 compatible. updated. 27 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Wasn't using user's specified delta_slices-- but now is!. Grazie, S. Torrisi!
26 Nov 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add opt -volreg_warp_final_interp This controls final interpolation for all non-NN warps, including catenated EPI transforms (affine and non-linear), final EPI, and anatomical followers. Done for "the boss".
25 Nov 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX) Dsets weren't found in places specified by env var. Fixed now.
23 Nov 2018, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL) Outputs JSON files now, for easier handling of information later. These provide more comprehensive info, as well as href linknames. 23 Nov 2018, P Taylor, apqc_make_html.py, level 3 (MAJOR), type 0 (GENERAL) Much better page formatting now, including navigation bar. User can jump to sections.
20 Nov 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL) Make subtxt fonts gray (oooh!) and uniformly bold. Also, made image links not be whole line (much more convenient). 20 Nov 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 1 (NEW_PROG) For use with @chauffeur_afni: subroutine that used to be *in* it. More modular and useful now, better selection of montage xhair loc, too. 20 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Fixed the calc of the location of xhairs when box_focus_slices was used. Should have correct focal location in montages now.
19 Nov 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE) add opt -html_review_style and run apqc_make_html.py
06 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX) Fixed delta-slice definition for 4D mode of imaging (occasional probs). Should have correct gapord values across all views now.
05 Nov 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) Alpha and Boxed now work with Clusterize 05 Nov 2018, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL) Adjust to keep up with new afni alpha/boxed behavior. Update internal calls to @chauffeur_afni, which needed new opts for this. 05 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-olay_alpha' and '-olay_boxed' for new alpha/boxed driving. Keepin' up with changes to afni driving, via RWC work.
02 Nov 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) Add 'A' and 'B' buttons on top of threshold slider To control Alpha and Boxed.
01 Nov 2018, P Taylor, 1dplot.py, level 3 (MAJOR), type 1 (NEW_PROG) New plotting program for 1D files. Copies much of the fun 1dplot capability to some pythonic realm.
21 Oct 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 1 (NEW_PROG) Helper program for afni_proc.py. Make @ss_review_html script for HTML version of AP QC. 21 Oct 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 1 (NEW_PROG) Helper program for afni_proc.py. Run @ss_review_html, build QC dir with html file for ss review. 21 Oct 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-pbar_saveim PBS' and '-pbar_dim PBD', to output color pbar. Just add in new AFNI driving functionality from RWC, to save colorbar.
19 Oct 2018, RW Cox, AFNI driver, level 2 (MINOR), type 6 (ENHANCE) Add PBAR_SAVEIM command to the driver repertoire
17 Oct 2018, RW Cox, TSV files, level 2 (MINOR), type 5 (MODIFY) Replace 'N/A' 'NaN' and 'Inf' with mean of other column values These strings will no longer stop a column from being marked as 'string' vs. 'number'.
16 Oct 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE) added new uvar fields Move g_ss_uvar_fields to lib_ss_review.py. Add uvar fields: nt_applied, nt_orig, ss_review_dset, pre_ss_warn_dset, decon_err_dset, tent_warn_dset. 16 Oct 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX) Maybe not really a bug, but this program wasn't work as it should have. It now should find NIFTI sets better, and use afnirc env vars.
15 Oct 2018, P Taylor, @djunct_slice_space, level 2 (MINOR), type 1 (NEW_PROG) Helper program for @chauffeur_afni. Calculate even spacing of slices for montaging. 15 Oct 2018, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 1 (NEW_PROG) Helper program for @chauffeur_afni-- wrapper of it for QC stuff. It's for alignment checking, and it's... edgy. 15 Oct 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-box_focus_slices REF', to avoid looking at empty slices. Can used a masked dset as REF to focus on certain slices only. 15 Oct 2018, P Taylor, 3dAutobox, level 2 (MINOR), type 2 (NEW_OPT) More new options Also output midslices, more info to screen (on-demand), and xyz stuff. 15 Oct 2018, P Taylor, 3dAutobox, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-extent_ijk_to_file FF'. Output IJK extents to a simple-formatted text file.
12 Oct 2018, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV) Longname support in AFNI atlases Environment variable AFNI_ATLAS_NAME_TYPE to control
09 Oct 2018, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX) fix decay rest with non-zero min; block unlimited decay stim dur Thanks to D Plunkett for noting the problem.
05 Oct 2018, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE) directly go after expected column headers in TSV files
20 Sep 2018, RW Cox, 3dttest++ etc., level 3 (MAJOR), type 6 (ENHANCE) ETAC now output global thresholds as well as local Global thresholds are text tables of cluster-size (or cluster-FOM) thresholds that apply to the whole volume in the multi-threshold way, rather than dataset tables that apply voxelwise. Moderately extensive hanges to programs 3dMultiThresh 3dXClustSim 3dttest++ and to support files mri_threshX.c thd_Xdataset.c 3dttest++ now has options to turn on/off global and local ETAC threshold calculations.
28 Aug 2018, P Taylor, @xyz_to_ijk, level 2 (MINOR), type 1 (NEW_PROG) Helper program to be able to convert xyz coors to ijk indices. Supplementary program.
27 Aug 2018, RW Cox, 1dsound and AFNI GUI, level 2 (MINOR), type 5 (MODIFY) modify sound output 1dsound now can make sound from up to 4 columns from input file. AFNI graph viewer GUI keypresses: p = play sound from central sub-graph P = play sound from central and average sub-graph (2 toned) K = kill running sound player Note that killing AFNI while sound is playing, or using K to kill sound, will leave a file whose name is like AFNI_SOUND_TEMP.something.au on the disk, and the user will have to clean it up.
23 Aug 2018, RW Cox, 1dsound, level 2 (MINOR), type 1 (NEW_PROG) program to generate .au sound file from a 1D file Very primitive at this moment.
22 Aug 2018, RC Reynolds, tedana_wrapper.py, level 2 (MINOR), type 5 (MODIFY) change exec_or_error() to use afni_util.py, which returns strings Thanks to J Gonzalez-Castillo for noting this python3 update.
20 Aug 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE) Play sound with 'p' or 'P' keypresses p = sound from central graph. P = sound from average of visible graphs. Sound is played via sox program (not part of AFNI). Environment variables: AFNI_SOUND_NOTE_TYPE sets type of note played AFNI_SOUND_GAIN sets loudness
17 Aug 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT) add option -write_uvars_json; add a few more user vars Add afni_ver, afni_package and final_epi_dset to uvars. Add 'AFNI version' and 'AFNI package' to review basic output. Add afni_util:write_data_as_json(), lib_vars_object:get_attribute_dict().
16 Aug 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_computed_uvars; set template
15 Aug 2018, RW Cox, 3dGrayplot, level 3 (MAJOR), type 6 (ENHANCE) Total rewrite of resampling from time+space to X+Y grid Grid refinement (time-X) is now cubic interpolation rather than linear Grid coarsening (space-Y) is now minimum sidelobe taper averaging rather than linear tapering 15 Aug 2018, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added functions for extracting version information from dataset HISTORY E.g. get_last_history_ver_pack(), get_last_history_version(). This file now depends on 're'.
14 Aug 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX) return a zero array on invalid parameters Thanks to E Silson for noting the problem.
10 Aug 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX) Allow non-stat bricks to be thresholded. Before, if the [ithr] brick was nonstat, crashing occurred.
07 Aug 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) if converting tedana.py results to standard space, include -space Thanks to L Dowdle for noting the problem.
31 Jul 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-check_abs_min ..'. Just allows the same-named opt from 1dDW_Grad_o_Mat++ to be used. 31 Jul 2018, P Taylor, @GradFlipTest, level 2 (MINOR), type 2 (NEW_OPT) New opt: '-check_abs_min ..'. Just allows the same-named opt from 1dDW_Grad_o_Mat++ to be used.
30 Jul 2018, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT) -percent and -range options For Cesar C-G. '-range X' sets the values to be plotted over the range -X..X (black..white). '-percent' is for plotting non-zero mean files, by converting them to percent of baseline (mean). Should be combined with '-range 4' (say).
25 Jul 2018, P Taylor, @chauffeur_afni, level 3 (MAJOR), type 0 (GENERAL) Several new options, as well as ability to deal with 4D images. Many new features, probably including minor bug fixes. 25 Jul 2018, P Taylor, @djunct_calc_mont_dims.py, level 2 (MINOR), type 4 (BUG_FIX) Was excluding solution of a square set of dimensions. Tested; seems fine now.
24 Jul 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE) version v1.0.20180622, including fix for enhanced DICOM Philips bvec/bval Update from C Rorden.
23 Jul 2018, RW Cox, AFNI driver, level 2 (MINOR), type 6 (ENHANCE) New command: SET_ULAY_RANGE For example: SET_ULAY_RANGE A.axialimage 0 200
05 Jul 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -mask_opts_automask Done for L Atlas.
01 Jul 2018, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT) New opt: well, actually, it is new to *have* explicit options now! Same great functionality, but with more flexible options/names/outputs. 01 Jul 2018, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL) Now respects including a path in the third argument (prefix/filename). Useful for scripting and selecting directory for output images.
26 Jun 2018, P Taylor, fat_proc_select_vols, level 2 (MINOR), type 4 (BUG_FIX) Bug fixed in supplementary program to *this* program. Used to get an error when no bad vols were selected. 26 Jun 2018, P Taylor, fat_proc_convert_anat, level 2 (MINOR), type 2 (NEW_OPT) Can provide a NIFTI file as input, not just a directory of dicoms. All niceifying steps can thus be applied to already-converted vol. 26 Jun 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT) New opt '-focus_by_ss' to do skullstripping before alignment stuff. Final dset is *not* skullstripped, but it helps with center of mass. 26 Jun 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 4 (BUG_FIX) Would return an error when *no* bad vols were selected. Note about fixing it in Jan, 2018; must have forgot to push that ver!
25 Jun 2018, P Taylor, fat_proc_select_vols, level 2 (MINOR), type 0 (GENERAL) The adjunct program, @djunct_dwi_selector.bash, was changed to be tcsh. No output diffs; but bash one couldn't run on new Mac OS (bad Mac)...
22 Jun 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE) version v1.0.20180614, including JPEG-LS support Update from C Rorden.
21 Jun 2018, RC Reynolds, model_PRF_6_BAD, level 2 (MINOR), type 1 (NEW_PROG) old model_PRF_6, but with version and gauss_file udpates This is for result comparison.
19 Jun 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX) fix rotation term, B should be 2*B Thanks to R Le, G Usabiaga and B Wandell for suggesting a review.
18 Jun 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 6 (ENHANCE) add AFNI_MODEL_PRF_GAUSS_FILE env var, to write image of Gaussian Done for model_conv_PRF and model_conv_PRF_6, should to _DOG, too. 18 Jun 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) more status 0 updates: file_tool, serial_helper
15 Jun 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY) update some programs so that -help is valid and return 0 Update 3dGrayplot 3dresample 3dretroicor @2dwarper @FSlabel2dset tokens.

auto-generated by afni_history on Jun 3 2020