AFNI HISTORY

all levels

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 -type NEW_OPT 

---- log of AFNI updates (most recent first) ---- 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.
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
10 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -niml_hdr, to write full NIML header(s) to stdout
07 Oct 2019, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Simpler opts for package and version number. For scriptability.
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.
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.
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.
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, @FindAfniDsetPath, level 1 (MICRO), type 2 (NEW_OPT) full_path option - full path for current path
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, 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, 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, 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, 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, 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.
20 Aug 2019, RW Cox, 3dPval, level 1 (MICRO), type 2 (NEW_OPT) Add -zscore option
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.
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
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.
24 Jul 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_tsv_label_details option
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.
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.
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, @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.
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, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) add -dset_extension, -storage_mode
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.
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.
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 2 (NEW_OPT) More pbar control: put in afni's '-XXXnpane P' behavior. Same option name used in this prog.
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_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.
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!
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.
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.
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.
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.
27 Mar 2019, RW Cox, @SSwarper, level 1 (MICRO), type 2 (NEW_OPT) -SSopt to add options to 3dSkullStrip For example: -SSopt '-o_ply Zhark.rules' to produce a brain surface in .ply format. [Per the request of Allison Nugent]
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.
26 Feb 2019, RW Cox, 3dPolyfit, level 1 (MICRO), type 2 (NEW_OPT) Option to save spatial fit coefficients Plus a little general cleanup of the code and help 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++.
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.
13 Feb 2019, P Taylor, @SSwarper, level 1 (MICRO), type 2 (NEW_OPT) Renaming the non-pre-skullstripping option to -init_skullstr_off. Otherwise, might falsely seem like NO skullstripping would be done.
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.
08 Feb 2019, RW Cox, @afni_refacer_run, level 1 (MICRO), type 2 (NEW_OPT) Add -deface option -- to remove face rather than replace it 08 Feb 2019, RC Reynolds, 3dWarp, level 1 (MICRO), type 2 (NEW_OPT) add -wsinc5
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 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.
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.
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
11 Jan 2019, RC Reynolds, dicom_hinfo, level 1 (MICRO), type 2 (NEW_OPT) add -sepstr option Done for ZXu on message board.
08 Jan 2019, RW Cox, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT) Add '-nolite' option For backwards compatibility and testing.
11 Dec 2018, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Also add -Quint30 and -lite options To run with reduced order polynomials, which are faster and appear to be about as accurate (as they should be, in asymptotic approximation theory).
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 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.
30 Oct 2018, RW Cox, AFNI, level 1 (MICRO), type 2 (NEW_OPT) -julian to print out the Julian date (who doesn't want this?)
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.
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, auto_warp.py, level 1 (MICRO), type 2 (NEW_OPT) at_opts for @auto_tlrc options
24 Aug 2018, RW Cox, 1dsound, level 1 (MICRO), type 2 (NEW_OPT) -notes option makes notes This is the default. Pentatonic notes with triangle waveforms.
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, 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'.
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).
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.
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.
01 Jun 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT) New pre-alignment opt, -pre_align_center_mass. Probably more useful than older -pre_center_mass. 01 Jun 2018, P Taylor, 3dClusterize, level 1 (MICRO), type 2 (NEW_OPT) New opt to output vols even if no clusters are found. These would be empty vols-- juuuust if the user wants.
30 May 2018, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 2 (NEW_OPT) User can specify matching cost and warp. How exciting is that?? (Well, mostly for test comparisons...).
29 May 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can crop the saved images. See the '-crop_*' options.
25 May 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add option -combine_opts_tedwrap, to pass to tedana_wrapper.py This is currently for passing -tedana_is_exec, say. Done for M Vaziri-Pashkam.
23 May 2018, RW Cox, 3dTfilter, level 1 (MICRO), type 2 (NEW_OPT) Updates to add capability Now can set half-width for despike as well as adaptive filter. Now can use adaptive detrending with new filter 'adetrend'. 23 May 2018, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add -ushort2float This will add the option to any to3d command via -gert_create_dataset. Done for H Brice.
21 May 2018, P Taylor, p2dsetstat, level 2 (MINOR), type 2 (NEW_OPT) Include '-bisided' as a type of test, explicitly. Same behavior as '-2sided', just easier for scripting.
17 May 2018, RC Reynolds, 3dNLfim, level 1 (MICRO), type 2 (NEW_OPT) add -help_models and -load_models This is easier than: '3dNLfim -DAFNI_MODEL_HELP_ALL=Y -signal eggs'.
16 May 2018, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 2 (NEW_OPT) added map_all option for the main 'use vol2surf?' plugin menu The 'map_all' option applies plugin parameters to all mappable surfaces, rather than applying defaults to any surface not specified as surf_A/B. This allows one to use normals and the various mapping functions. Done for D Glen.
15 May 2018, RC Reynolds, tedana.py, level 1 (MICRO), type 2 (NEW_OPT) add --seed, update for modern numpy New option --seed can be used for regression testing. Use integer subscripts in arrays; replace some '== None' with 'is None'.
08 May 2018, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) add multi-echo combine methods: OC_tedort, tedana_OC, tedana_OC_tedort With this, afni_proc.py can run tedana.py and extract projection components (projecting good orts from bad, making cleaner bad orts). OC_tedort : like AFNI's OC, but also regress clean orts tedana_OC : tedana.py's OC tedana_OC_tedort : tedana.py's OC, and regress clean orts The tedort (orthogonalized tedana projection components) terms are applied in the regress block, still as per-run terms.
07 May 2018, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 2 (NEW_OPT) add -ver, -meica_dir, -work_dir, init history
28 Apr 2018, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT) add option -stop_gap and map functions nzave, nzmode, median, nzmedian
18 Apr 2018, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -csim_show_clustsize and helper options to report cluster requirements Given a cluster table output by 3dClustSim, use this option to extract the mininum cluster size, given uncorrected and corrected p-values. Use -csim_pthr and -csim_alpha to specify those respective p-values.
12 Apr 2018, RC Reynolds, 3dMVM.R, level 1 (MICRO), type 2 (NEW_OPT) add -verb option
04 Apr 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -combine_opts_tedana, to pass opts down to tedana.py
03 Apr 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) initial testing run with -combine_tedana_path
19 Mar 2018, RW Cox, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) Add -MSSD and -MASD option MSSD = mean successive squared differences (Von Neumann) MASD = median absolute successive differences
15 Mar 2018, P Taylor, fat_proc_convert_dwis, level 2 (MINOR), type 2 (NEW_OPT) Can provide NIFTI+bvec+bval files as inp, not just a directory of dicoms. All niceifying steps can thus be applied to already-converted vol.
01 Mar 2018, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT) add -oc_method (OC_A, OC_B) OC_B: compute T2* from full log() time series, rather than log(mean(TS)). 01 Mar 2018, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) add -combine_method cases of OC_A and OC_B
26 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add option -help_section, and use it to add some missing option help
23 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add option for running OC combine method, use '-combine_method OC' This will run the current method implemented in @compute_OC_weights. This is probably a bit of a test, as I expect to modify the base 'OC' method, and therefore add other related names. 23 Feb 2018, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT) add option -echo_times, for convenient use by afni_proc.py
22 Feb 2018, RC Reynolds, 3dMean, level 2 (MINOR), type 2 (NEW_OPT) add option -weightset to compute a weighted sum This N-volume weight dataset is used to apply voxelwise weights to the N input datasets, one volumetric weight to each dataset. The motivated example is combining single runs (at a time) of multi-echo data with the weights generated by @compute_OC_weights. 22 Feb 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Can now apply p-to-stat calcs for thresholding. User gives p-value, which gets made to appropriate stat for thresh.
16 Feb 2018, RW Cox, 3dTcorr1D, level 1 (MICRO), type 2 (NEW_OPT) New -dot option (dot product) 16 Feb 2018, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) add combine block and ability to process multi-echo data Have new options -dsets_me_echo and -dsets_me_run for input. Still need to implement OC and ME-ICA. Thanks to L Atlas and J Gonzalez-Castillo. 16 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add option -mask_epi_anat, to apply tigher mask in place of full_mask By default, create epi_anat intersection mask.
15 Feb 2018, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) add showproc option to exec_tcsh_command(), to show command and text
06 Feb 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT) Can put a ceiling on the final output volume: -do_ceil_out. Reduce impact of tiny spikes (often at fringe) later on.
01 Feb 2018, RW Cox, AFNI GUI, level 3 (MAJOR), type 2 (NEW_OPT) -bysub option for reading from BIDS hierarchy -bysub 10506 (for example) means to find all sub-directories with names 'sub-10506', and read all datasets find in them and in THEIR sub-directories into a single session. The idea is to make it easy to read all datasets corresponding to a single subject from a BID hierarchy into a single session, for easy of viewing. 01 Feb 2018, RC Reynolds, 3dTto1D, level 2 (MINOR), type 2 (NEW_OPT) add methods 4095_count/frac/warn Count 4095 values, or warn if datum is short and max is 4095.
30 Jan 2018, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 2 (NEW_OPT) add -help_concerns, to describe some general concerns regarding timing
18 Jan 2018, DR Glen, 3dUndump cubes, level 1 (MICRO), type 2 (NEW_OPT) -cubes makes cubes instead of spheres
22 Dec 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -select_runs and -mplaces For B Benson and A Harrewijn, see Example 18d. 22 Dec 2017, P Taylor, fat_proc_connec_vis, level 2 (MINOR), type 2 (NEW_OPT) Can output the intermediate tstat or tcat files of ROI maps. Might be useful in subsequent volumetric analyses.
20 Dec 2017, RW Cox, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) -Tslices lets user replace slice time offsets I don't know why this didn't exist before. So now the user can attach slice time offsets to a dataset if they weren't correct before (e.g., in NIFTI files).
02 Nov 2017, RW Cox, aiv, level 1 (MICRO), type 2 (NEW_OPT) -pad option makes all images the same size for viewing
01 Nov 2017, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 2 (NEW_OPT) implement the decay_fixed distribution type See make_random_timing.py -help_decay_fixed for details.
31 Oct 2017, RW Cox, 3dMultiThresh, level 2 (MINOR), type 2 (NEW_OPT) Add -allmask option, to see which case(s) caused a positive Add then used in 3dttest++ to produce the ETACmaskALL output dataset
05 Oct 2017, RW Cox, 3dTsort, level 1 (MICRO), type 2 (NEW_OPT) add -ranFFT option, for Cesar
04 Oct 2017, RW Cox, 3dTsort, level 1 (MICRO), type 2 (NEW_OPT) add -random option = shuffle each time series independently
21 Sep 2017, RW Cox, 3dXClustSim, level 1 (MICRO), type 2 (NEW_OPT) Allow user to set -minclust (instead of fixed at 5)
20 Sep 2017, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 2 (NEW_OPT) New opt to push through tiny, negative diagonal elements in bmatrices. Useful-- but use this option cautiously, and look at your data...
19 Sep 2017, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) add -line option for drawing arbitrary line segments
12 Sep 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -multi_timing_3col_tsv and -write_multi_timing Also, add -multi_show_duration_stats for married timing files. This is to process 3 column TSV (tab separated value) formatted timing files, as might be found in the OpenFMRI data.
30 Aug 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -fsl_timing_files and -write_as_married This is for converting FSL timing files to AFNI format.
22 Aug 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -apply_end_times_as_durations and -show_duration_stats For B Benson and P Vidal-Ribas.
17 Aug 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Some new labelling, etc. optioning. Make some new labels, locationing based on XYZ and more.
16 Aug 2017, P Taylor, afni, level 1 (MICRO), type 2 (NEW_OPT) Added color map (applies to both afni and suma): Reds_and_Blues_Inv So, new color opt readily available.
08 Aug 2017, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 2 (NEW_OPT) Can have surfaces, niml.dsets and spec files move along with vols. Added capability to mapping volume dsets.
20 Jul 2017, RW Cox, 3dFWHMx, level 3 (MAJOR), type 2 (NEW_OPT) Require -ShowMeClassicFWHM to get the Forman FWHM estimates Otherwise, these results are shown only as zeros. The intention is to make it harder to use an archaic model for the noise spatial correlation. But not to break afni_proc.py, which expects 4 values to be output there.
13 Jul 2017, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT) Add '-NNx' options to specify clustering method -NN1 or -NN2 or -NN3 These can replace the use of 'rmm' and 'vmul', and are meant to make using this program simpler and more compatible with Clusterize in the AFNI GUI.
11 Jul 2017, DR Glen, DriveSuma quiet variable, level 1 (MICRO), type 2 (NEW_OPT) SUMA_DriveSumaQuiet Make suma a little quieter with DriveSuma
03 Jul 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT) Some new subbrick-setting optioning. For utilizing 'SET_SUBBRICKS i j k' functionality in driving afni.
19 Jun 2017, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) add -assume_dicom_mosaic to handle Siemens 3D format Done for A. Jahn.
06 Jun 2017, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT) New inflation opt: '-skel_stop_strict'. Think this might be useful: don't expand at all *into* WM skel.
12 May 2017, P Taylor, 3dDWItoDT, level 3 (MAJOR), type 2 (NEW_OPT) Added goodness-of-fit measures to '-debug_brik' output. Two chi-sqs from Papadakis et al. (2003); thx, J Ipser for idea.
09 May 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) apply -offset for advanced case (remove from todo list)
04 May 2017, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT) Allow box-y neighborhoods. User can input values for cubic/prism neighborhoods now. 04 May 2017, P Taylor, 3dDTtoDWI, level 2 (MINOR), type 2 (NEW_OPT) Added in '-scale_out_1000' option, to match 3dDWItoDT. This allows it to be used with scaled tensors from 3dDWItoDT.
01 May 2017, RC Reynolds, @diff.files, level 2 (MINOR), type 2 (NEW_OPT) add option -diff_prog, to use something besides xxdiff
27 Apr 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) With '-output_mask_nonnull', user can output mask of non-null ts. This was made to help those who need to finnd null time series here. 27 Apr 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) With '-ts_wb_strlabel', can use ROI string labels in WB output filenames. This was made expressly for The Rajendra Who Shall Not Be Named.
26 Apr 2017, RW Cox, 3dMultiThresh, level 1 (MICRO), type 2 (NEW_OPT) Add option to choose sign for 1-sided thresholding
19 Apr 2017, DR Glen, 3dMean min, max options, level 2 (MINOR), type 2 (NEW_OPT) 3dMean computes min and max voxelwise across datasets Options -min, -max give min and max values. This can be combined with -non-zero to restrict to non-zero min and max. 19 Apr 2017, DR Glen, 3dLocalstat has_mask, has_mask2 options, level 2 (MINOR), type 2 (NEW_OPT) 3dLocalstat can report if neighborhood intersects specified values Options -has_mask and -has_mask2 allow flagging with unfillvalue
05 Apr 2017, DR Glen, 3dVol2Surf nzoptions, level 2 (MINOR), type 2 (NEW_OPT) 3dVol2Surf nonzero min, nonzero max, nonzero ave Options allowing for statistics that ignore zero values
30 Mar 2017, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) simple statistics of filled or unfilled These options provide binary tests for whether the neighborhood shape entirely fits within a mask or dataset around each voxel A value can be specified for a fill and unfill value
27 Mar 2017, RC Reynolds, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT) add -write_dist, for writing a distortion vector dataset After running something like: MapIcosahedron ... -write_dist test.dist to create test.dist.lh.sphere.reg.gii.txt, get summaries with: 1d_tool.py -collapse_cols euclidean_norm -show_mmms \ -infile test.dist.lh.sphere.reg.gii.txt
03 Mar 2017, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) add optimally combined 'Opt Comb' merge method Done with V Roopchansingh.
01 Mar 2017, RW Cox, 3dUnifize, level 3 (MAJOR), type 2 (NEW_OPT) Add -EPI option, to unifize time series datasets.
28 Feb 2017, RW Cox, 3dEmpty, level 1 (MICRO), type 2 (NEW_OPT) Add -geom option = define dataset by a 'MATRIX(...)' string
03 Feb 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) decay timing class now follows better distribution; new decay_old class
27 Jan 2017, P Taylor, 3dDWItoDT, level 1 (MICRO), type 2 (NEW_OPT) Miniscule new option, '-bmatrix_FULL' to have clearer usage. Just copies functionality of cryptic '-bmatrix_Z'.
26 Jan 2017, RC Reynolds, Makefile.macosx_10.7_local, level 2 (MINOR), type 2 (NEW_OPT) this is a new Makefile to prep for exec directory dynamic linking
18 Jan 2017, RW Cox, 3dmerge, level 1 (MICRO), type 2 (NEW_OPT) option -nozero will prevent output of an all zero dataset
11 Jan 2017, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 2 (NEW_OPT) added some help: -help_advanced, -help_todo
30 Dec 2016, RW Cox, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT) Add -ACF option -- to compute ACF parameters from residuals
26 Dec 2016, P Taylor, thd_center, level 2 (MINOR), type 2 (NEW_OPT) Extra argument in THD_cmass() and THD_roi_cmass(). Allows for local ijk coordinate output; updated other calling functions.
23 Dec 2016, P Taylor, 3dCM, level 2 (MINOR), type 2 (NEW_OPT) Allow ijk coordinate output. Will be in local orientation. Makes undumping after easier.
21 Dec 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add '-wmask' option Like '-wball', enhances the auto-generated weight in a region, but this region is selected by a mask dataset.
20 Dec 2016, P Taylor, fat_mvm_prep.py, level 1 (MICRO), type 2 (NEW_OPT) New --unionize_rois option: affects GRID element selection. Now can select union of matrix elements across group for MVM_tbl.
08 Dec 2016, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 2 (NEW_OPT) add -digits and -keep_datum; other minor updates
18 Nov 2016, RC Reynolds, @Align_Centers, level 1 (MICRO), type 2 (NEW_OPT) add -prefix option, to name output
17 Nov 2016, DR Glen, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Ask suma to send current surface name to SUMA_OUTPLUG file or stdout
09 Nov 2016, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) add -gert_chan_prefix Done for W Luh.
01 Nov 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add PPI preparation options Add -regress_skip_censor to omit 3dD -censor option. Add -write_ppi_3dD_scripts with corresponding options -regress_ppi_stim_files and -regress_ppi_stim_labels. These make PPI pre and post regression scripts, along with the main analysis script. Done for S Haller.
09 Oct 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) new options -mask_import, -mask_intersect and -mask_union For J Stoddard and J Jarcho.
29 Sep 2016, RW Cox, 3dDespike, level 2 (MINOR), type 2 (NEW_OPT) -NEW25 is a slightly more agressive approach (a) uses 25 point running median instead of 9 for pre-filtering (b) sets cut2=3.2 (4 MADs) instead of 4.0 (5 MADs)
28 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -regress_ROI[_PC]_per_run options, to make per-run regressors Also, used 3dTproject to detrend PC regressors for appropriate censoring.
23 Sep 2016, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -select_runs option
19 Sep 2016, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) add glob2stdout, for converting glob forms to lists in stdout 19 Sep 2016, RC Reynolds, @move.to.series.dirs, level 1 (MICRO), type 2 (NEW_OPT) add -glob, for processing glob forms via afni_util.py and xargs
16 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -radial_correlate option, to run @radial_correlate in proc script
14 Sep 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Have a new '-bmax_ref ...' option: if bref has b>0. Won't have much effective change *yet*, but will later. Possibly.
13 Sep 2016, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) add -blip_opts_qw to pass options to 3dQwarp in the blip block 13 Sep 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT) New opt -bref_mean_top to average over mean bref when b>0. Also, totally reprogrammed most of interior; had been too scraggly.
23 Aug 2016, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT) add -fix_rich_quotes; if fixing a script, convert rich quotes to ASCII Done for G Chen.
05 Aug 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -marry_AM Added for J Wiggins.
20 Jul 2016, RW Cox, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT) -tempdir for -Clustsim
08 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add -read_all, in case it is useful for sorting (e.g. -order_as_zt) Added for K Vishwanath.
07 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) add -order_as_zt to re-order from -time:tz to -time:zt
24 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -requires_afni_hist; warp vr_base to make final_epi dset
22 Jun 2016, RC Reynolds, @diff.tree, level 1 (MICRO), type 2 (NEW_OPT) added -diff_opts; e.g. -diff_opts -w 22 Jun 2016, RC Reynolds, @diff.files, level 1 (MICRO), type 2 (NEW_OPT) added -diff_opts; e.g. -diff_opts -w
21 Jun 2016, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT) Add -perc option for percentile
14 Jun 2016, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT) Option -FWHMdset allows specifying per-voxel blurring parameter For use with 3dLocalACF and scripting. EXPERIMENTAL! 14 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -blip_forward_dset; if needed copy along any obliquity information
13 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -align_unifize_epi : 3dUnifize EPI before anat alignment Thanks to D Glen and S Torrisi for suggesting it. 13 Jun 2016, DR Glen, 3dTstat - single sub-bricks, level 2 (MINOR), type 2 (NEW_OPT) For datasets with only a single sub-brick, 3dTstat would exit with an error for many statistics. The new behavior makes the program use the first value of the time series instead. Some other requested statistics like the argmax type stats are now calculated even for this trivial case. Optionally the user may use -firstvalue for a statistic
10 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -blip_reverse_dset for blip up/blip down distortion correction
03 Jun 2016, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) -wtprefix to save computed weight to dataset
27 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Have a new '-scale_out_1000' option: rescale output, if desired. Effectively: change output diff units of mm^2/s -> x10^{-3} mm^2/s.
20 May 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) add options -dot_file_list/_pack/_show List, package (tgz) or show the contents of found 'dot' files.
19 May 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) -wball = emphasize some (spherical) region in the weighting Written in Hangzhou China -- for Peng
16 May 2016, DR Glen, align_epi_anat.py - left/right test, level 2 (MINOR), type 2 (NEW_OPT) left/right checking using align_epi_anat.py flipped datasets go unnoticed even in major publicly available databases (initially noted by Brad Buchsbaum with FCON1000). Now automatically determine mismatch in L/R with simple test New -check_flip and -flip_giant options check alignment against flipped data.
06 May 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT) -XXXnpane to set number of panes in pbar For the elusive ZXu, man of many nations.
05 May 2016, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Option -percentile P Computes the Pth percentile 0 <= P <= 100 of the data in each voxel. Can only be used once per run!
03 May 2016, DR Glen, @Atlasize no voxel regions, level 1 (MICRO), type 2 (NEW_OPT) Skip structures with no voxels New -skip_novoxels option in @Atlasize and @MakeLabelTable
02 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Have a new '-min_bad_md' option: use to threshold badness. Also now detect bad DT fits if MD is crazy big. Whoa.
28 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) add -local_package, to use an already downloaded package Requested by P Taylor.
08 Apr 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT) Add '-XXX defaults'
07 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) add options -proto and -test_proto One can specify the download protocol as http, https or NONE.
05 Apr 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) fix bug with -5final -- but still hide from user 05 Apr 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 2 (NEW_OPT) New inp format option-- for dealing with TORT export/import. -bmatrix_Z for reading in bmat in AFNI format; byebye -bmatr opt. 05 Apr 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT) New I/O options-- for dealing with TORT export. Now have I/O of grad columns weighted by bvalues.
29 Mar 2016, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT) add option -no_cert_verify, to skip server certificate verification
25 Mar 2016, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT) A bunch of '-XXX' options to control colors and fonts
24 Mar 2016, RW Cox, afni GUI, level 1 (MICRO), type 2 (NEW_OPT) Add -XXX option Moving towards letting user set X11 things (fonts, colors) on the command line. Still needs work, but has some functionality now for the true Jedi AFNI Master. 24 Mar 2016, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) add option -use_obl_origin, to apply -oblique_origin to to3d command Also, run any to3d script via 'tcsh -x' so the users get to see.
21 Mar 2016, RC Reynolds, GLTsymtest, level 1 (MICRO), type 2 (NEW_OPT) added -badonly, to avoid screen clutter from many good GLTs
22 Feb 2016, RW Cox, debugtrace.c, level 1 (MICRO), type 2 (NEW_OPT) Colorize WARNING and ERROR message prefixes. Can turn off by setting AFNI_MESSAGE_COLORIZE to NO. For Javier.
11 Feb 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT) -clustsim option This option runs 3dttest++ with -randomize and then 3dClustSim with -inset, to produce cluster-threshold tables for inclusion in the output. It is my intention that this method will replace the use of 3dFWHMx and 3dClustSim. Knock wood, and help Make AFNI Great Again! 11 Feb 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT) Add -ztest option == test inputs if they are all zero For Cesar.
09 Feb 2016, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT) -read option To 'read()' data in, instead of 'mmap()' -- for network mounted data where 'mmap()' fails to work. For Cesar Caballero.
05 Feb 2016, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT) New -inset option Directly give the simulations, rather than generate them internally. Intended for use with '3dttest++ -randomsign N -toz' and '3dttest++ -resid' to get the cluster thresholds directly from the data rather than assumptions of Gaussianity.
22 Jan 2016, RW Cox, 1deval, level 1 (MICRO), type 2 (NEW_OPT) Fixed value assignments, as in '-a=3.7' For my convenience 22 Jan 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) rigid_body alignment option and better handling of user allineate options
06 Jan 2016, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) new -pnm option, to save to PNM image format To make it easier to manipulate results in scripts (e.g., pnmcat).
30 Dec 2015, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 2 (NEW_OPT) add -acf option, to estimate FWHM via the ACF method
07 Dec 2015, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) Add -resid option, to save residuals.
01 Dec 2015, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT) Added -acf option! Non-Gaussian spherically symmetric AutoCorrelation Function (ACF) for the noise. Uses FFTs to create the noise fields, via #include-d file mri_radial_random_field.c and #include-d csfft_OMP.c (thread-safe FFTs). This method in 3dFWHMx and 3dClustSim will be the favored cluster thresholding analysis going forward.
16 Nov 2015, P Taylor, 3dTrackID, level 3 (MAJOR), type 2 (NEW_OPT) Can limit tracts to 'between targets' in new ways. See '-targ_surf_stop' and '-targ_surf_twixt' in the help.
10 Nov 2015, RW Cox, 3dFWHMx, level 3 (MAJOR), type 2 (NEW_OPT) -ACF option to compute spatial autocorrelation function For enhancing 3dClustSim, et cetera.
06 Nov 2015, RC Reynolds, @Align_Centers, level 1 (MICRO), type 2 (NEW_OPT) add option -cm_no_amask; like -cm but without -automask
04 Nov 2015, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) add -slice_order_to_times This converts a list of slice indices (sorted by acq time) to slice times (ordered by index).
28 Oct 2015, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) add -dodice, to get the Dice coefficient
21 Oct 2015, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added -exec
01 Sep 2015, DR Glen, 3dcalc extreme, absextreme, level 2 (MINOR), type 2 (NEW_OPT) New extreme and absextreme operators to find extreme values
20 Aug 2015, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_isi_pdf and -show_isi_f_pdf
19 Aug 2015, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_missing, to show all missing labels from all files
12 Aug 2015, RC Reynolds, @radial_correlate, level 1 (MICRO), type 2 (NEW_OPT) add -mask option, to apply instead of automask Done for Giri.
11 Aug 2015, RW Cox, 3dFWHMx, level 2 (MINOR), type 2 (NEW_OPT) -1difMOD option Computes the moments of the 1st differences, then estimates the mean and standard deviation of the smoothness factors, then reports the mean smoothness adjusted upwards to allow for the fact that 3dClustSim depends more strongly on bigger smoothness than on smaller smoothness. For use with single subject tests; probably too conservative for group analyses.
10 Aug 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 2 (NEW_OPT) Minor new option: input list of ROIs with file. For minor convenience.
07 Aug 2015, RC Reynolds, 3dhistog, level 1 (MICRO), type 2 (NEW_OPT) add -noempty option, to ignore empty bins
29 Jul 2015, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) add -nzstdev option Given a voxel, extract all the values. Throw out those values that are nonzero. Compute the stdev of the remaining set (assuming at least 2), with no further processing (no detrending).
27 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) -dsort_nods option When used with -dsort, this option will make 3dREMLfit calculate the results with the -dsort regressors(s) omitted as well as the results with the -dsort regressor(s) included -- so the user can compare the dsort and non-dsort results easily with 1 run of the program. 'nods' == 'no dsort'. Each nods dataset will have the string '_nods' appended to the prefix.
23 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Add -dsort option Allows the addition of voxel-wise baseline regressors. To test out ANATICOR applied to task-based FMRI data, for example.
11 Jul 2015, RC Reynolds, @diff.files, level 1 (MICRO), type 2 (NEW_OPT) added -longlist
07 Jul 2015, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 2 (NEW_OPT) Simple new option to exclude x-axis labels. They might just be annoying.
01 Jul 2015, RC Reynolds, cifti_tool, level 2 (MINOR), type 2 (NEW_OPT) reorg and more recur functions
24 Jun 2015, RC Reynolds, afni_xml_tool, level 2 (MINOR), type 2 (NEW_OPT) afni_xml updates, and start to afni_xml_tool
18 Jun 2015, RC Reynolds, 3dExtrema, level 2 (MINOR), type 2 (NEW_OPT) added -nbest Output -nbest extrema; -quiet does not suppress extrema output.
17 Jun 2015, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT) added functions for reading from a buffer
15 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -disp_cext
06 Jun 2015, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -per_run_file
05 Jun 2015, RW Cox, 3dSimARMA11, level 1 (MICRO), type 2 (NEW_OPT) Add hidden -tdof option
01 Jun 2015, RC Reynolds, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT) added -dupe_ok and more warnings when dataset labels match
26 May 2015, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add secret -tdof option
22 May 2015, DR Glen, 3dLocalstat mode, level 2 (MINOR), type 2 (NEW_OPT) Find mode and non-zero mode in voxel neighborhood
21 May 2015, P Taylor, 3dDWUncert, level 1 (MICRO), type 2 (NEW_OPT) Can choose to analyze only high-FA voxels: don't waste time on GM/CSF. Option to ignore low-FA vox for uncert, leave them 0.
18 May 2015, RC Reynolds, gen_ss_review_table.py, level 1 (MICRO), type 2 (NEW_OPT) mention gen_ss_review_scripts.py -help_fields in help
15 May 2015, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT) Can output separate bval file. Useful in some TORT preprocessing.
14 May 2015, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add -demean option == remove mean from time series before plotting Multiple -demean options implies higher order polynomials!
08 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_make_corr_vols Use this to compute average correlation volumes for various masks.
04 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -anat_follower, -anat_follower_ROI, -regress_anaticor_label
30 Apr 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) allow AM2 centering param via basis backdoor (for now) For example, use basis function 'BLOCK(2) :x:0.176' Done for J Britton.
28 Apr 2015, DR Glen, to3d - do not write BRIK, level 1 (MICRO), type 2 (NEW_OPT) Do not write binary data with -nowritebrik May be useful for faster realtime acquisition with symlinks
23 Apr 2015, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 2 (NEW_OPT) add -help_fields[_brief], to describe the 'basic' output fields
14 Apr 2015, RC Reynolds, uber_subject.py, level 1 (MICRO), type 2 (NEW_OPT) add MIN_OUTLIERS as an option for volreg base
02 Apr 2015, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added ctrl+l and ctrl+L to globally dim/brighten lighting 02 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -tlrc_NL_warped_dsets to import 3dQwarp result Added for P Molfese and others.
01 Apr 2015, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) anat followers and ROI_PC Datasets can follow the anatomical warps Added options -regress_ROI_PC, -regress_ROI_maskave, -regress_ROI_erode. PC allows for some number of principle components to be regressed, and maskave is for mask averages to be regressed. The _erode option applies to either, and happens before xform. Also, any anat with skull is applied as a follower. Also, -tcat_remove_first_trs can now take a list.
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Selection now possible on VR rendered image in SUMA
23 Mar 2015, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT) Add -singletonA option For testing one subject vs a collection of 'normals'. Works with covariates.
18 Mar 2015, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT) Added -node_depth 18 Mar 2015, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT) Added options -in_range, -ex_range for thresholding and output COM and Cent These changes resulted in numerous small changes throughout the code for a more uniform handling of thresholding methods
13 Mar 2015, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Added ExistsAs in ParseName This can find whether or not you have datasets on disk with some view (+tlrc), say given only a prefix. 13 Mar 2015, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) added option -te_list to pass ECHO_TIMES to plug_realtime
12 Mar 2015, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) Added -pc* and -key options to compute coordinate PC of clusters. See -help for details.
11 Mar 2015, ZS Saad, 3dSeg, level 3 (MAJOR), type 2 (NEW_OPT) Added -mixfloor to avoid getting NAN when certain classes disappear. Also added -mixfrac IGNORE to turn off any modulation by the mixing fraction during the EM routines.
04 Mar 2015, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Added WHelp button to mimic BHelp but open online pages This required a few additional modifications to the auto-help generating functions. Lots of work under the hood.
27 Feb 2015, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -regress_WMeL_corr option, which I forgot about last time 27 Feb 2015, RC Reynolds, @compute_gcor, level 1 (MICRO), type 2 (NEW_OPT) added -corr_vol, to output a global correlation volume Note that afni_proc.py does these steps by default.
26 Feb 2015, ZS Saad, IsoSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -autocrop and -mergerois+dset See help for details 26 Feb 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 2 (NEW_OPT) Added -no_zero_attraction See help for details
25 Feb 2015, ZS Saad, IsoSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -remesh option to simplify meshes 25 Feb 2015, ZS Saad, IsoSurface, level 1 (MICRO), type 2 (NEW_OPT) Added auto dset generation along with surfaces with -isorois+dsets
23 Feb 2015, ZS Saad, IsoSurface, level 3 (MAJOR), type 2 (NEW_OPT) Made IsoSurface handle ROI volumes better See options -mergerois, -isorois for details 23 Feb 2015, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Set transparency and rendering modes per object See ctrl+o, ctrl+p 23 Feb 2015, ZS Saad, suma-general, level 1 (MICRO), type 2 (NEW_OPT) Added support for STL I/O format. It is handy for 3D printing.
17 Feb 2015, DR Glen, align_epi_anat.py center alignment, level 2 (MINOR), type 2 (NEW_OPT) -ginormous_move and -align_centers added Added call to @Align_Centers for initial center alignment The -align_centers option can be used by itself with the transformation matrix included in the combination transformation. Adding the center alignment on to giant_move, given the nom of ginormous_move. Note these options ignore any obliquity in the original datasets.
12 Feb 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_anaticor_fast/-regress_anaticor_fwhm This implements the 'fast' ANATICOR method, computing the WMeLocal voxel-wise regressors via an FWHM Gaussian sum of WMe voxels, rather than a uniform sum within a radius. 12 Feb 2015, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT) added -no_consec option, to block consecutive events
09 Feb 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) Can threshold bundles with too few tracks; TRK files not default out. Useful to control false pos; useful to save space outputting.
06 Feb 2015, ZS Saad, 3dSurfMask, level 1 (MICRO), type 2 (NEW_OPT) Added -meth peri to return intersection with surface only.
05 Feb 2015, ZS Saad, 3dinfill, level 1 (MICRO), type 2 (NEW_OPT) Added -mask option to restrict filling to holes within mask 05 Feb 2015, ZS Saad, 3dBrickStat.c, level 1 (MICRO), type 2 (NEW_OPT) added -stdev
02 Feb 2015, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Take coords from a surface rather than just a file for -com node_xyz
30 Jan 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 2 (NEW_OPT) Added -vol_skin and -vol_hull to create smooth contours of mask volume. 30 Jan 2015, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT) Improvements to SOLID fill method and addition of option -ed
26 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) Can dump output *maps*, not just masks, of each connection. See '-dump_rois AFNI_MAP' for how it works.
23 Jan 2015, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Added -stat list and -stat hist* .
21 Jan 2015, ZS Saad, 3dGenPriors, level 1 (MICRO), type 2 (NEW_OPT) Made program output centrality measures with -do o . Documentaiton hidden until option is ready for mass usage.
20 Jan 2015, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added option -show_trs_to_zero, to compute length of iresp This is to computer the number of TRs until a curve bottoms out at 0.
16 Jan 2015, ZS Saad, 3dHist, level 1 (MICRO), type 2 (NEW_OPT) Added -get outl Included fixing returned values in SUMA_hist_value() when out of bounds.
15 Jan 2015, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT) -zero_wrap, and -gray_wrap for padding with black, white, or gray levels. 15 Jan 2015, ZS Saad, @ExamineGenFeatDists, level 1 (MICRO), type 2 (NEW_OPT) Added option -nx, padding with white, fixed couple of small glitches too. 15 Jan 2015, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT) added -hist; if unknown opt and cur version, fail after check
13 Jan 2015, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Secret option '-ballopt' A step towards using more complex basis functions, by allowing optimization only over an L2-ball in parameter space, rather than a hypercube.
07 Jan 2015, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add -gridlist and -allsave options Allows specifying the exact list of patch/grid sizes to use, and also to save the output warp at each level. 07 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) Switch to output nifti files. For PAIRMAP, INDIMAP and -dump_rois output. 07 Jan 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT) Switch to output nifti files. For GM and GMI files. 07 Jan 2015, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) Switch to output nifti files. For corr map or Z map files.
22 Dec 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added All Objs button to initialize controllers for all objects if desired
18 Dec 2014, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT) Add -T2 option
15 Dec 2014, P Taylor, 3dROIMaker, level 3 (MAJOR), type 2 (NEW_OPT) Make a subset of an ROI by choosing maximal neighoring values. Start with peak value, add neighboring max until N voxels selected.
10 Dec 2014, ZS Saad, imcat, level 2 (MINOR), type 2 (NEW_OPT) Added -autocrop* options
04 Dec 2014, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Added -handedness option. 04 Dec 2014, DR Glen, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT) 1Dmat_only_nodset option Undid former fix because other scripts may rely on these shifted datasets and added new option. Datasets will not be output or modified with new option, and just the transformation matrix is output
26 Nov 2014, ZS Saad, 3danisosmooth, level 2 (MINOR), type 2 (NEW_OPT) Output of diffusion measures, along with adjustment of debug volumes For details, see tersely named option -save_temp_with_diff_measures, along with modified help for -savetempdata
25 Nov 2014, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added get_process_depth() sample use: afni_util.py -print 'get_process_depth()'
05 Nov 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) Switch to not output INDI and PAIR map files. In connectome examples, this might save a lot of space.
17 Oct 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -load_masks, -save_masks, and -masks for driving tract controller Options help in creating all GUI help and herald the automation of the tract and tract masking controller.
16 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added sort_methods: none, acq_time, default, num_suffix, zposn
15 Oct 2014, ZS Saad, imcat, level 2 (MINOR), type 2 (NEW_OPT) Added -respad_in, -gscale, and -pad_val options Proces involved modifications to mri_read_resamp_many_files(), mri_zeropad_2D(), and a new mri_valpad_2D(). See imcat -help for details.
10 Oct 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added directions and point clouds as DOs See interactive help for #directions, #points 10 Oct 2014, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT) -realaxes ==> use ijk_to_dicom_real vs. ijk_to_dicom
07 Oct 2014, ZS Saad, AFNIio.R, level 2 (MINOR), type 2 (NEW_OPT) Allowed specification and inheritance of TR in write functions
03 Oct 2014, RW Cox, 3dTsmooth, level 1 (MICRO), type 2 (NEW_OPT) Add adaptive mean filtering as an option
30 Sep 2014, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Now show bundles labels recently added to FATCAT
26 Sep 2014, P Taylor, 3dTrackID, level 3 (MAJOR), type 2 (NEW_OPT) Allow labeltable reading and writing. This allows users to use labeltables, and output labelled values everywher e. 26 Sep 2014, P Taylor, 3dNetCorr, level 3 (MAJOR), type 2 (NEW_OPT) Allow labeltable reading and writing. This allows users to use labeltables, and output labelled values everywher e.
24 Sep 2014, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added -list2 case under -listfunc
23 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Allowed interactive cluster thresholding by node number (-ve Area value) Previously this was possible only via command line's -n option. Command line now also supports negative -amm2 values if -n is not set. 23 Sep 2014, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added some explicit -help and improved the few existing options
22 Sep 2014, ZS Saad, 3dGenFeatureDist, level 2 (MINOR), type 2 (NEW_OPT) Added -hspec to explicitly set histogram generation parameters
18 Sep 2014, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 2 (NEW_OPT) Allow interaction terms in the user-defined statistical model. Allow cat+quant or cat+cat variable interactions, and posthoc testing.
17 Sep 2014, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -pc_proj and -node_depth options. These options are meant to help localizing seeds along DBS electrodes. Relevant C code functions: SUMA_NodeDepth(), SUMA_Project_Coords_PCA() and SUMA_*_PC_XYZ_Proj()
16 Sep 2014, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT) added -fill_dirs option, to specify directions for hole filling Added for D. Glen.
08 Sep 2014, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT) Allow pre-inflation of an input ROI, at user request. Useful, for example, if wanting to go from WM->GM.
29 Aug 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added -drive_com to allow the driving of SUMA by its command line
28 Aug 2014, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT) Added -equalized to do histogram equalization on the whole volume
26 Aug 2014, RW Cox, 3dNwarpApply and 3dNwarpCat, level 1 (MICRO), type 2 (NEW_OPT) Add '-expad' option for extra padding, if needed for some reason
25 Aug 2014, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Added -*PrefixView, and improved -out to multi-components
22 Aug 2014, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -sort_method and -save_details Using the 'geme_index' sort method allows for real-time sorting of GE multi-echo data, before volumes are sent to 'afni'. Modification made for V Roopchansingh.
07 Aug 2014, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Add -pblur option, for progressive blurring That is, more blurring at coarse levels and less blurring at fine levels. May become the default after some more experience.
05 Aug 2014, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Made program handle FreeSurfer's -contrasurfreg output
04 Aug 2014, P Taylor, 1dDW_Grad_o_Mat, level 3 (MAJOR), type 2 (NEW_OPT) Can edit dataset with averaging B0s and DWIs. Should make life easier for dual processing of vecs and datasets. 04 Aug 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) New option for PAIRMAP labelling by X, not 2^X; new *.grid NT scaling. Make PAIRMAP easier to view; user wanted extra matrices. 04 Aug 2014, P Taylor, 3dDWUncert, level 1 (MICRO), type 2 (NEW_OPT) Internal options for testing uncertainty things. For internal testing only at this point.
02 Aug 2014, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT) added -run_trs, for cases when the TRs per run vary Requested on message board by Rebecca and later by Lisam.
31 Jul 2014, ZS Saad, 3dpc, level 1 (MICRO), type 2 (NEW_OPT) Added option -nscale to scale covariance matrix by number of samples This would make output consistent with R and matlab decompositions Also changed output files names for 1D files to make program not clobber results in .1D mode
18 Jul 2014, ZS Saad, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Added option -nscale to avoid scaling with byte/short output 18 Jul 2014, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT) Add -iwarp option, to invert the result from -nwarp
17 Jul 2014, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Made ROIgrow work with single node ROIs, see help for -node_labels PER_NODE
16 Jul 2014, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Fixed bug with computation of tract_P0_offset_private values
15 Jul 2014, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added different ways to highlight masked tracts
10 Jul 2014, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) -hist option for plotting histogram style
09 Jul 2014, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Mean b=0 values computed for linear estimate New -mean_b0 option allows for averaging of b=0 values used in linear model and initial linear estimate for nonlinear method.
07 Jul 2014, RW Cox, 3dNwarpXYZ, level 1 (MICRO), type 2 (NEW_OPT) Add -iwarp option to allow for warp inversion For a few points, should be MUCH faster than using 'INV(warp)' for the -nwarp option.
30 Jun 2014, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) Add -lpc and -lpa options Sounds simple, but was really a lot of work to make these reasonably efficient. And to work at all, for that matter. Ugh.
27 Jun 2014, RW Cox, 3drefti, level 1 (MICRO), type 2 (NEW_OPT) Add -checkaxes option
26 Jun 2014, RC Reynolds, 3dresample, level 2 (MINOR), type 2 (NEW_OPT) added -bound_type FOV/SLAB option (FOV is orig and default) FOV preserves the field of view, SLAB preserves the SLAB (so with SLAB the extents should not change)
19 Jun 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) Added new feature: output partial correlation matrices. Can output r-like and beta-like partial correlation matrices.
07 Jun 2014, ZS Saad, auto_warp, level 2 (MINOR), type 2 (NEW_OPT) Made -dataTable options take text file instead of command line opts This makes it possible to have very large tables without exceeding limit on command line length. File name has to begin with '@' in keeping with some C-language 3d progs.
02 Jun 2014, ZS Saad, auto_warp, level 2 (MINOR), type 2 (NEW_OPT) Added -qworkhard and -qw_opts for finer control of 3dQwarp step
21 May 2014, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Option -iname to give filename as appearing on the command line
19 May 2014, RC Reynolds, column_cat, level 1 (MICRO), type 2 (NEW_OPT) added -line option, e.g. to print only (0-based) line 17
12 May 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_use_tproject, and made the default=yes This will apply 3dTproject instead of 3dDeconvolve for resting state analysis. It is much faster, and creates the same result.
09 May 2014, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -part_init option; removed -chrono option
02 May 2014, RW Cox, afni, level 1 (MICRO), type 2 (NEW_OPT) add -papers option, to list AFNI papers The list of papers is maintained in file afni_papers.txt which is turned into afni_papers.h via program quotize.
29 Apr 2014, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT) Freedom in neighbor defs; also can keep just N peak values per ROI. User can specify face, edge or vertex ngbs. Also, search for N max vals. 29 Apr 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) Added new feature: output WB correlations as Zscores. Can output WB maps of ROI average time series correlations as Z-scores.
24 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Reading of OBJ file format for triangular meshes. 24 Apr 2014, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) add -ssave:TYPE option for saving the volumes as dataset 24 Apr 2014, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -multi_timing_to_event_list This allows one to generate simple or details event lists, or to partition one event class by its predecessors. Partitioning added for W Tseng.
21 Apr 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT) Added new feature: do whole brain correlations. Can output individual WB maps of ROI average time series correlations. 21 Apr 2014, P Taylor, 1dDW_Grad_o_Mat, level 1 (MICRO), type 2 (NEW_OPT) Output grads as rows-- new option switch. Done at user request.
17 Apr 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -controller_position to position object controller window
10 Apr 2014, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -index_to_run_tr, intended for use by afni_proc.py
08 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added 'F10' to toggle prying axis between Z and Y
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added three modes for controlling how connections to a node are shown. This makes it possible to greatly reduce the clutter of the display. See menu 'CN' that controls this 04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) A double select click makes all graph edges appear. This only has an effect if the current object in focus is a graph object 04 Apr 2014, DR Glen, whereami -linkrbrain, level 2 (MINOR), type 2 (NEW_OPT) New option for getting task or gene correlation with coordinate list Linkrbrain.org support is available in alpha form from whereami and the Clusterize GUI. AFNI_LINKRBRAIN needs to be set to YES to use new features.
02 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Made AFNI's crosshair changes move tract mask in SUMA This happens when the viewer is in Mask Manipulation Mode.
31 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -anat_unif_GM (def=yes); improved message for bad ricor input
28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added 'F11' to allow users to set the object rendering order This is an interactive version of env: SUMA_ObjectDisplayOrder 28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Implemented doppleganger for masks on pried surfaces 28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added prying along the horizontal direction too This is most handy when you want to travel along the lateral surface and still see what gives in tracts or on slices.
27 Mar 2014, ZS Saad, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) Added -overwrite for Stephen Robinson
26 Mar 2014, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Wrote a new function to handle input events New function SUMA_RecordEvent() records X events into a structure that I can clone and attach into the Pick Results struct. Without this, I can't tell down the line if a pick was with shift+control or without it. A problem when deciding what to tell AFNI, for example The new functions (see also SUMA_ShftCont_Event() and other functions around it should replace all queries in SUMA_input() about event qualifiers. Still need to check about handling of button swap, or conditions when drawing, etc. 26 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Made double-click right click outside of objects turn off mask movement 26 Mar 2014, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT) Shift+Control+right click in SUMA will trigger Instacorr refresh in AFNI This way you can click on an object in SUMA and still get AFNI to so a volumetric ICOR computation, with all accompnaying talk back to SUMA. etc.
25 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -anat_uniform_method and -anat_opts_unif This correction may be particularly useful along with either -tlrc_NL_warp or -mask_segment_anat.
24 Mar 2014, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) -useweight is now the default; -noweight turns it off 24 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_anaticor_radius This specifies the radius for the local white matter average. Option requested by S Torrisi.
21 Mar 2014, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) added -data_root and enhancements for class data search
13 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) More improvements to multiple object transparency. There's lots more than meets the eye. See comment in functions SUMA_DrawVolumeDO_3D() and SUMA_StippleMask_shift() 13 Mar 2014, ZS Saad, afni_open, level 2 (MINOR), type 2 (NEW_OPT) A few more tweaks, like -aw and -d See afni_open -help for details
07 Mar 2014, RC Reynolds, afni, level 1 (MICRO), type 2 (NEW_OPT) added -no_detach, to prevent detaching from the terminal Useful since -DAFNI_DETACH=NO cannot work as written.
06 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added option to make rendered slices jump to new cross hair location See new function SUMA_VO_set_slices_XYZ() for details 06 Mar 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT) Changes for reading in DTI files. Allow NIML-formatted input file, as well as globbing in ordinary case. 06 Mar 2014, P Taylor, 3dDWUncert, level 2 (MINOR), type 2 (NEW_OPT) Changes for reading in DTI files. Allow NIML-formatted input file, as well as globbing in ordinary case.
05 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Fixed initial setting of masks to be relative to center of tracts object This required creation of SUMA_ADO_Center() and SUMA_ADO_Range() functions .
25 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added loading/saving of masks and evaluation expressions to GUI. 25 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added tract length masking in Masks GUI. 25 Feb 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) Added -dset_labels option to label dset sub-bricks. Normally 3drefit would handle that, but not for graph dsets, not yet at least 25 Feb 2014, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Secret option for Javier to make graph dsets display on top of everything The option is hidden for now, requiring the use of both -dev and a temporary env. The two can be combined on the command line with: suma -dev -setenv "'JAVIER_DEPTH_SPECIAL = YES'" ...
19 Feb 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -Clst and -UseClst options to DriveSuma
18 Feb 2014, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -test_local_timing, to look for local vs. global timing issues - in some cases, promote married types to combine/compare them - keep track of '*' entries from timing files
06 Feb 2014, RW Cox, 3dttest++, level 1 (MICRO), type 2 (NEW_OPT) -nomeans AND -notests to shut off more of the output
03 Feb 2014, RC Reynolds, apsearch, level 1 (MICRO), type 2 (NEW_OPT) added -global_help/-gopts_help to print help for global options
29 Jan 2014, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) -brickwise allows time-dependent t-test results For Stephen Robinson
08 Jan 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) Added -graph_XYZ_LPI to flip coords to RAI for the user.
27 Dec 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_tr_run_counts and -show_num_runs, for gen_ss_review_scripts.py
23 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added option to hide graph nodes when nothing is connected to them 23 Dec 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added support for F12 key from DriveSuma
17 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Allowed graph node coloring based on a graph point's group ID To use such a coloring scheme, set Cl --> Grp in the surface controller for a graph dataset. To set group IDs and color, see ConvertDset's option -graph_named_nodelist_txt 17 Dec 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) ConvertDset's -graph_named_nodelist_txt now takes node grouping and color See -graph_named_nodelist_txt's help section for details
16 Dec 2013, RC Reynolds, auto_warp.py, level 2 (MINOR), type 2 (NEW_OPT) added -qblur option for P Molfese
11 Dec 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Wildcard file expansion with extension and view trimming and sorting See apsearch's -help output with all the -wild_* options for detail. Functions at the heart of all this are unique_str() and MCW_wildcards(). 11 Dec 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Added -afni_web_downloader Done via GetAfniWebDownloader()
06 Dec 2013, RW Cox, 3dTproject, level 1 (MICRO), type 2 (NEW_OPT) Add new NTRP censor mode, just for the Spaniard. Where are my cookies?
04 Dec 2013, RW Cox, 3dDespike, level 1 (MICRO), type 2 (NEW_OPT) Add -dilate option
03 Dec 2013, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) added -prog_list for Ziad
29 Nov 2013, RW Cox, 3dDespike, level 2 (MINOR), type 2 (NEW_OPT) add -NEW option Different fitting method than L1 -- much faster, results not identical, but does that matter for an ad hoc algorithm?
27 Nov 2013, ZS Saad, 3dCM, level 2 (MINOR), type 2 (NEW_OPT) Added -roi_vals to get COM for multiple ROIs Workhorse is THD_roi_cmass() in thd_center.c
15 Nov 2013, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) Add -stim_times_FSL option Allows scripting from FSL-style timing files, as distributed by the Human Connectome Project. God Save the Queen.
31 Oct 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_trs_run This will be used by afni_proc.py to restrict TRs for blur estimation to those that were not censored, per run.
23 Oct 2013, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add -xtran option (to complement -ytran)
21 Oct 2013, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT) Add -xmulti option For graphing with different x-values for different y-value 1D files. 21 Oct 2013, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) And the -dashed option
18 Oct 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) added -weight option
19 Sep 2013, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) show label->sub-brick index conversion via AFNI_SHOW_LABEL_TO_INDEX 19 Sep 2013, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT) added options -get_processed_env[_afni] and -global_opts
16 Sep 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Switched functions of mouse buttons 1 and 2 when viewing GRAPH MATRIX This means matrix spatial rotation would be done with button 2 and shifting with button 1. Selection can also be done with button 3 whenever there is no selectable surface in sight.
11 Sep 2013, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allow for surface specification with symbolic notation Option -i now can parse strings like: ld60:MNI_N27:l:smoothwm to load surfaces from template volumes that would be stored in the afni data directory (see THD_datadir()). Also the -spec option can now take such symbolic notation 11 Sep 2013, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT) Added -afni_data_dir to get the location of the data directory
03 Sep 2013, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Text annotation of graph dset representation with shadows.
28 Aug 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) -allinkeep option ==> keep -allineate files around
26 Aug 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) added -check_all, -find_prog, -casematch, -exact These changes are to add PATH searching for programs.
20 Aug 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_RSFS, to run 3dRSFC Would run 3dRSFC per run on errts, to bandpass and compute parameters.
14 Aug 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added non-linear standard space registration via -tlrc_NL_warp
05 Aug 2013, ZS Saad, inspec, level 2 (MINOR), type 2 (NEW_OPT) Added -remove_state to remove surfaces of specific state from spec file
31 Jul 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -xmat_1D NegXY to flip X Y coordinate sign of surfaces. This should make it easy to turn GIFTI files with RAI units to LPI with something like: ConvertSurface -i toy.gii -o_gii toy -overwrite -xmat_1D NegXY 31 Jul 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -merge_surfs to facilitate ECOG strip merging.
19 Jul 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) -resample and -allinfast options For resampling (without registering) and fast affine registering -- both done via 3dAllineate.
16 Jul 2013, RW Cox, 3dQwarp, level 3 (MAJOR), type 2 (NEW_OPT) -allineate = run 3dAllineate first With this option, 3dQwarp can align datasets that are not so close, and are not on the same 3D grid (since the substitute source dataset output by 3dAllineate will be on the base grid).
09 Jul 2013, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT) added -ushort2float, for converting unsinged shorts to floats Requested by D Handwerker.
01 Jul 2013, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT) added AFNI_INCLUDE_HISTORY: set to No to omit history from output
28 Jun 2013, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added get/show_process_stack(), get/show_login_shell() Can use these from command line, e.g. : afni_util.py -eval 'show_login_shell()' afni_util.py -eval 'show_login_shell(verb=1)' afni_util.py -eval 'show_process_stack()'
27 Jun 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_mot_as_ort Applies motion regressors via -ortvec, a potential future change.
25 Jun 2013, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT) Add -ssave option, to save scaling dataset for perusal 25 Jun 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -volreg_motsim and -volreg_opts_ms
07 Jun 2013, RW Cox, 3dhistog, level 1 (MICRO), type 2 (NEW_OPT) Add -igfac option To ignore scale factors -- to histogram-ize the underlying shorts or bytes in a dataset.
04 Jun 2013, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) Added nearest neighbor search option There is no need to search along a certain direction when mapping between two speres of identical radius and size.
24 May 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Add -noneg option, to crush negative values in input datasets.
14 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT) New -plusminus option 'Meet-in-the-middle' matching: base(x-dis(x)) = source(x+dis(x)). For application to unwarping blip-up and blip-down EPI datasets. Also, fix bug when -no?dis options are used -- when the code for parameter sub-vector mapping was moved around, the 'free' call to get rid of any old mapping wasn't moved with it -- bad Bob, bad bad bad. 14 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added options -show_argmin/max
09 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -write_3dD_script and -write_3dD_prefix
08 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added options -rank, -rank_style, -reverse_rank
07 May 2013, RW Cox, 3dQwarp, level 1 (MICRO), type 2 (NEW_OPT) Add -Qfinal option (experimental)
06 May 2013, RW Cox, 3dNwarpApply, level 1 (MICRO), type 2 (NEW_OPT) Add -short option == save results as shorts For use in warping label datasets. 06 May 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) added option -slice_timing 06 May 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added option -transpose_write
03 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -regress_anaticor and -mask_segment_erode Use the -regress_anaticor option to regress the WMeLocal time series. This is the ANATICOR method of HJ Jo.
26 Apr 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_trs_censored/_uncensored (mostly for X-matrix datasets)
24 Apr 2013, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -censor_next_TR Sticking with backward diff for deriv, as it makes sense for censoring.
22 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Added -out1D option to output correlations in text format.
19 Apr 2013, DR Glen, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT) lpi xyz output option
16 Apr 2013, RC Reynolds, 3dmaskave, level 2 (MINOR), type 2 (NEW_OPT) added -sumsq (sum squares) and -enorm (Euclidean norm) options
09 Apr 2013, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added options for providing orts for each input time series See options -*_orts in the help output.
04 Apr 2013, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -Apair option For testing differences in correlations in 1 group from 2 different seeds -- the regular seed minus the 'Apair' seed. Also changes to AFNI to set the Apair seed, etc.
01 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 1 (MICRO), type 2 (NEW_OPT) Added option -mask_source
27 Mar 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_group_labels, -label_prefix_keep/_drop Option -label_prefix_drop can be used to remove bandpass regs for 3dRSFC. 27 Mar 2013, DR Glen, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT) absolute value of voxels for statistics
26 Mar 2013, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added option -inflate for automatic creation of semi-inflated surfaces See @SUMA_Make_Spec_FS -help for details 26 Mar 2013, ZS Saad, SurfSmooth, level 1 (MICRO), type 2 (NEW_OPT) Added -match_center to force recentering of smoothed surfaces. SurfSmooth -help for details 26 Mar 2013, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) Add option -cmeth (MEAN or MEDIAN) for Steve Gotts
25 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Merged handling of CoordBias with Prying, all in VisX Lots of annoying little details there. See functions like: SUMA_*CoordBias*, SUMA_ApplyVisXform(), and SUMA_Apply_VisX_Chain() 25 Mar 2013, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT) More voxelwise neighborhood shapes available. Voxelwise neighborhoods can be any sphere/radius size, and even ellipsoidal. Some memory stuff should be better as well.
22 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added stippling for line segments DOs, see SUMA's ctrl+h for details.
14 Mar 2013, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) NearestNodeCoords was added to -output_params 14 Mar 2013, ZS Saad, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) -init_xform now takes AUTO_CENTER_CM and CENTER_CM
12 Mar 2013, RW Cox, 3dNwarpApply, level 2 (MINOR), type 2 (NEW_OPT) Various fixes -ainterp = lets you interpolate data differently from warp -affter = lets you use a different affine warp for each sub-brick -nwarp = allow catenation and inversion directly on the command line These last 2 options make the program 3dNwarpCat pleonastically redundant. 12 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) Handling input and output directories Output now goes to current directory (./) unless otherwise specified with -output_dir. Thanks a lot, Rick.
11 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) Handling input and output directories Output follows input directories unless specified with -output_dir Previously, all input files had to exist in current directory. Changes allow for output to follow anat or epi dataset directories or specified output directory. Also minor change to call tcsh without sourcing startup .cshrc 11 Mar 2013, DR Glen, @Atlasize center of mass, level 2 (MINOR), type 2 (NEW_OPT) Add -centers for center of mass locations in atlas regions -centers option added to @Atlasize and @MakeLabelTable This location is simple center of mass for now and may be outside region for non-blobbish regions
08 Mar 2013, RC Reynolds, 3dTcat, level 2 (MINOR), type 2 (NEW_OPT) added -TR and -tpattern options
27 Feb 2013, RW Cox, 3dUnifize, level 1 (MICRO), type 2 (NEW_OPT) Added -GM option to stretch gray matter to a consistent-ish place 27 Feb 2013, RC Reynolds, python-general, level 1 (MICRO), type 2 (NEW_OPT) added Ziad's apsearch global options: -all_opts, -h_find, -h_view
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Prying hemispheres apart to see medial or lateral sides simultaneously This is controlled via the ctrl+Button 1-Motion. See SUMA's ctrl+h output for details. The prying behaviour is different for spheres and flat maps Just try it and see. ctrl+double click to get back to initial view. See also env: SUMA_LHunify 22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Automatically adjust position of LR surfaces so that they don't overlap This is only done for anatomically incorrect surfaces, the others should not overlap of course. This allows for simultaneous viewing of inflated surfaces and flattened ones side by side. 22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Option -anatomical labels all -i_* -t_* surfs anatomically correct 22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Option -onestate put all -i_* surfs on command line in the same state 22 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT) Instead of just individual ROI masks, can get map of Ntracks/voxel. This allows a posteriori thresholding/comparisons/analysis.
15 Feb 2013, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Added -FNameNoAfniExt to -out option 15 Feb 2013, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Allowed script to work with NIFTI input for both -surf_anat and -exp_anat
14 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Added stippling-based transparency to surface viewing. Fancier blending-based transparency will have to wait. 14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 2 (NEW_OPT) Option -nocor to improve data import from FreeSurfer Option avoid COR images, produces NIFTI and GIFTI output that aligns with the initial volume passed to FreeSurfer. This required considerable changes to the script and will not be the default for a while longer. 14 Feb 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -TransMode to control surface transparency. 14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 1 (MICRO), type 2 (NEW_OPT) Option -set_space set space of output volumes 14 Feb 2013, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT) Add -emask option (exclude certain voxels) For use in registering pre- and post-surgery volumes (e.g.).
07 Feb 2013, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) Added Greg Baxter's (UCSD) change for b-matrix input
06 Feb 2013, ZS Saad, MakeColorMap, level 2 (MINOR), type 2 (NEW_OPT) -suma_cmap, -usercolutfile, and -sdset* options for SUMA colormaps The new options allow users to create SUMA's colormaps with labels and turn datasets into labeled datasets with the user's colormap 06 Feb 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) -labelize for assigning a SUMA colormap to an integral valued dset 06 Feb 2013, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added special filename '1D:stdin' to make mri_read get 1D from stdin In this manner, most 3d programs can now accept stdin input in 1D format This change was suggested by Isaac Schwabacher. 06 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT) Add ability to output each WM-region mask as an individual ROI. This should make it simpler to use an ROI as a mask than with the 2^(ROI number) labelling system within subbrick outputs.
22 Jan 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Added -bash option for bash filename completion, & -recreate_all_afni_help Thanks be to Isaac Schwabacher. 22 Jan 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -echo_nel(*) option to show NIML communication elements 22 Jan 2013, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Added -hand for handeness of orientation 22 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -file_type, in prep for reading AFNI/NIfTI images
16 Jan 2013, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT) added option -dc_params To go with new scripts AFNI_data6/realtime.demos/demo.2.fback.*. 16 Jan 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added option -show_gcor (and _all and _doc) compute GCOR (average correlation) on 1D files
11 Jan 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) Added -flip_orient option to change orientation of triangles.
09 Jan 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added option -regress_compute_gcor If errts and EPI mask exist, GCOR is computed by default.
07 Jan 2013, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT) Added -radial_* options to test SUMA_Volume_RadFill() function. 07 Jan 2013, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) added option -l2norm, to compute L2 norm
27 Dec 2012, RW Cox, 3dPolyfit, level 1 (MICRO), type 2 (NEW_OPT) Add '-base' option To allow fitting (in space) arbitrary input images, as well as (spatial) polynomials.
26 Dec 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) -virtvec option for Javier
21 Dec 2012, ZS Saad, @clip_volume, level 1 (MICRO), type 2 (NEW_OPT) Added options -crop_allzero and -crop_greedy.
18 Dec 2012, ZS Saad, cat_matvec, level 1 (MICRO), type 2 (NEW_OPT) option -4x4 to output augmented matrix.
28 Nov 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) -dospcov Compute Spearman correlation of subject results with covariate. Output sub-bricks are labeled with '_SP' at the end, as in 'LLL_cov_SP' to indicate the group with label 'LLL' correlated with the covariate with label 'cov'. This is for the IMom (PK).
26 Nov 2012, RC Reynolds, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) added -save_script option added script history in afni_com class
15 Nov 2012, RC Reynolds, 3dTqual, level 2 (MINOR), type 2 (NEW_OPT) added -mask option Requested by evangelou.
12 Nov 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT) Straight and weighted divisions of T1 by PD, and initial alignment The weighted volume allows one to keep the high-res. aspect of PD division, while considerably reducing the extreme enhancement. 12 Nov 2012, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT) Added -cmask and -quiet to 3dHist
06 Nov 2012, ZS Saad, 3dkmeans, level 2 (MINOR), type 2 (NEW_OPT) Added -write_dists to only output ascii files when users want them The changes were made to also cleanup the output of 3dSeg. 06 Nov 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 2 (NEW_OPT) Added -head*, and -cut_below options to generate whole head masks This was needed because 3dAutomask or 3dSkullStrip would fail atcreating w hole head masks for cases with coil-array shading problems and/or lots of noise.
17 Oct 2012, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT) added -no_length option, which helps when running diffs on output
16 Oct 2012, ZS Saad, 3dSurfMask, level 1 (MICRO), type 2 (NEW_OPT) Option -no_dist to avoid length distance computations. Also, the fast method was improved per the comment below. 16 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added analysis type and processing block list
15 Oct 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT) A better masking option using -brainhull The option seems pretty good at creating brain mask from pretty lousy data.
13 Oct 2012, ZS Saad, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) -voxvol returns a voxel's volume in mm cubed
10 Oct 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added yoking of 1_only, Dim, and Opacity controls 10 Oct 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -Opa to control opacity 10 Oct 2012, ZS Saad, @RetinoProc, level 1 (MICRO), type 2 (NEW_OPT) Option -AEA_opts for passing arguments to align_epi_anat.py
09 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allow input of surface-based complex time series. SUMA will report and graph the magnitude of complex data Other transformations can be added when needed. Surface data I/O were modified to allow handling of complex-typed data including functions in thd_niml.c, and thd_gifti.c Programs like 3dDFT and 3dcalc can read/write complex surface- based datasets. 09 Oct 2012, ZS Saad, 3dDFT, level 2 (MINOR), type 2 (NEW_OPT) Allow handling of complex surface-based data Earlier versions could not output complex data for surface-based datasets. Minor changes to the help output to fix order of -cx2r option and allow option suggesting.
05 Oct 2012, RC Reynolds, dicom_hinfo, level 2 (MINOR), type 2 (NEW_OPT) added option -no_name 05 Oct 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added option -quick_censor_count
04 Oct 2012, ZS Saad, afni-matlab, level 2 (MINOR), type 2 (NEW_OPT) Minor tweaks to WriteBrik and BrikInfo WriteBrik can automatically set some header fields (AdjustHeader option) BrikInfo now loads IJK_TO_DICOM_REAL
28 Sep 2012, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) Enabled automatic centering via -init_xform You can use -init_xform AUTO_CENTER or -init_xform CENTER to perform center alignment during registration. 28 Sep 2012, ZS Saad, 3dTrackID, level 1 (MICRO), type 2 (NEW_OPT) Option -rec_orig to record dataset origin in tractography output
26 Sep 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT) added -apsearch; verify download for recursive step
19 Sep 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -scale option for the Person from Kolkata
13 Sep 2012, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT) Added -pdf to 3dhistog to make area = 1
07 Sep 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) SUMA now highlights cluster |max|, rather than max
06 Sep 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added -no_volreg for time series already registered 06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT) apply global opt -pad_to_node when going through AFNI format in thd_niml.c
05 Sep 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT) Added possiblity to scale by top percentiles with -FATscl This would produce .sc9 outputs. It looks like the scaling is more promising than by MEDIAN(20) or MAD(20). 05 Sep 2012, ZS Saad, 1dRplot, level 2 (MINOR), type 2 (NEW_OPT) Made program take in histograms produced by 3dGenFeatureDist This required changes to AFNIio.R so that NIML groups are not automatically sent to the distbin. Instead, the first element in the ni_group is returned. 05 Sep 2012, ZS Saad, 3dGenFeatureDist, level 1 (MICRO), type 2 (NEW_OPT) Program now creates the feature correlation matrix per class. Both histograms and correlation matrices are stored in NIML format under a directory named by the user.
04 Sep 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) Made program output niml 1D format, makes it easy to plot with 1dRplot 04 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added option -regress_ROI This allows for tissue-based regression, with ROI averages from any of: brain (from full_mask), GM, WM and CSF (from Classes_resam) The 'mask' block is required for all ROIs, and option -mask_segment_anat is required for the latter 3.
31 Aug 2012, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) added option -signed_absmax Requested by P Hamilton.
30 Aug 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) Made program create corr. matrix as opposed to just one pair of sub-bricks Output is also beautified with option -show_labels
29 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Allowing yoking of intensity to node selection. Ctrl+Button-3 would select a node and switch intensity sub-brick to that node's index * K. This is only done if the dataset currently viewed has as K times as many sub-bricks as the surface has nodes. K being an integer, naturally. Nick Oosterhoff instigated this business
28 Aug 2012, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Preserved controller settings for newly loaded or reloaded dsets The preserved settings include clustering options.
24 Aug 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Added interactive clustering to surface controller The state of affairs: -Clustering tables are only output to the terminal and the log window. -Clustering is yoked between hemispheres -Can control connectivity radius and min area or min nodes -When you click on a node inside a cluster, the node in that cluster with the highest value is highlighted with a black sphere. 24 Aug 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT) Added coordinate feature generation, if TLRC xform is provided Note that the TLRC xform need not be too precise. The coordinate features are not intended to make sure of segmentation templates. 24 Aug 2012, ZS Saad, SurfClust, level 1 (MICRO), type 2 (NEW_OPT) Allow -i* form of surface input
23 Aug 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT) can pass -censor_dset
21 Aug 2012, RC Reynolds, slow_surf_clustsim.py, level 1 (MICRO), type 2 (NEW_OPT) added 'sigma' uvar, for passing to SurfSmooth
20 Aug 2012, ZS Saad, SurfExtrema, level 1 (MICRO), type 2 (NEW_OPT) Made default input the convexity of the surface
15 Aug 2012, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) Added -sublabel_prefix and -sublabel_suffix
14 Aug 2012, DR Glen, whereami minimum probability, level 2 (MINOR), type 2 (NEW_OPT) Minimum probability option to consider for probabilistic atlases Can set option, -min_prob, or environment variable, AFNI_WHEREAMI_PROB_MIN, to control output of whereami reports or masks from probabilistic atlases
08 Aug 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -use_slice_loc; fixed app of use_last_elem in mri_read_dicom g_info.use_last_elem has usurped the lone global
30 Jul 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_mmms Display min, mean, max, stdev of each column.
26 Jul 2012, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_comm_times option to show communication times Added for J Evans (and to get it off an ancient todo list). 26 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -mask_segment_anat and -mask_rm_segsy If anat is stripped, create segmented anat unless user says not to.
19 Jul 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) Allow for L/R hemi yoking for many operations These include:Threshold setting. I,T,B sub-brick selection. Range setting. Dset loading. Cmap changing. Dset switching. Order changing.
12 Jul 2012, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) added ':a:b:c' appendage to -stim_times_AM2 To allow user to specify what values to subtract from modulation parameters (over-riding the default subtraction of the average).
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Use ArrowFields when datasets have large numbers of sub-bricks The switch is done automatically and is controlled with env: SUMA_ArrowFieldSelectorTrigger
29 Jun 2012, RC Reynolds, prompt_user, level 1 (MICRO), type 2 (NEW_OPT) if MESSAGE is '-', read from stdin
28 Jun 2012, ZS Saad, ROIgrow, level 2 (MINOR), type 2 (NEW_OPT) Added -insphere and -inbox options These options grow ROIs by finding nodes that fall inside a box or sphere of preset size around nodes in the original ROIs.
27 Jun 2012, RC Reynolds, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) added -nzmedian, requested on message board
22 Jun 2012, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) added commands 3dANOVA2 and 3dANOVA3; added option -factors Need to add help for -factors (i.e. for 3dANOVA3 -type 4).
19 Jun 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -switch_cmode to allow switching how values map to colors This controls the 'Col' menu in SUMA's surface controller.
15 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_censor_extern
24 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) csf_val and csf_fa options apply to linear solutions too
23 May 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Allow label-based selection for annotation files See function: process_NSD_labeltable(), now you can do something like: 3dcalc -a std.60.lh.aparc.a2009s.annot.niml.dset'' \ -expr 'step(a)' -prefix wm_lh_G_precentral.niml.dset 23 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -clust option, to allow 3dClustSim stuff to be used
22 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added regress_bandpass and regress_mot_deriv (probably for resting state) 22 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT) csf_val and csf_fa options for default values if B=0 less than gradient values
21 May 2012, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT) Made program output mapping info file for use with SurfToSurf Also made microscopic improvement to automatic dset name generation for -d set_map 21 May 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Made the script also port thickness data and take them to std. space 21 May 2012, ZS Saad, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) Added -covariance option, turned off DOF setting for anything but pearson. See function THD_covariance() 21 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added the long-desired-but-not-so-needed -regress_stim_types option This allows users to specify -stim_times/_AM1/_AM2/_IM.
17 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -donocov option When -covariates is used, -donocov says to also do the NO covariates analyses and tack them onto the end of the results -- for comparison fun
15 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT) Added '[1dcat FF.1D]' syntax for sub-brick selections in 1D file This was added for the same reason '[count ...]' was added, and that is to allow for lengthy selection values. Dealing with selections of 100+ sub-bricks virtually guarantees some string limit is reached, somewhere. See 3dTcat -help for details 15 May 2012, ZS Saad, 1dRplot, level 1 (MICRO), type 2 (NEW_OPT) Added -load.Rdat to regenerate previous plot on command line
08 May 2012, ZS Saad, count, level 2 (MINOR), type 2 (NEW_OPT) Added -form to count: count -form %c 49 130 08 May 2012, RW Cox, 1ddot, level 1 (MICRO), type 2 (NEW_OPT) Add -rank option to do Spearman correlations 08 May 2012, DR Glen, 3dinfo, level 1 (MICRO), type 2 (NEW_OPT) gen_space option to see generic space type for a dataset
07 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added weighted_enorm method for -collapse_cols; added -weight_vec 07 May 2012, DR Glen, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) out_space option to force output space for auto-talairached data
04 May 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added inverse distance measures to InstaCorr For the moment, those options are only accessible to usernames rwcox and ziad. Relevant functions are: THD_vectim_distance(), and THD_distance(). THD_distance() is not used at the moment, it would be from 3dLocalBistat once I get around to testing it. For now, its access from 3dLocalBistat is #if-ed out. 04 May 2012, RW Cox, 1dBport, level 1 (MICRO), type 2 (NEW_OPT) Add -quad option = linear and quadratic trend regressors
03 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -backward_diff and -forward_diff Note, -backward_diff is the same as -derivative.
27 Apr 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added percentile thresholding to AFNI's interface Relevant functions: flush_vinfo_sort(); flush_3Dview_sort(); get_3Dview_sort(); AFNI_thresh_from_percentile() Relevant structure variables: cont_perc_thr in Three_D_View; th_sort, N_th_sort, th_sortid in AFNI_view_info; Feature also accessible from plugout_drive with: SET_FUNC_PERCENTILE +/-
26 Apr 2012, RW Cox, 3dLocalBistat, level 2 (MINOR), type 2 (NEW_OPT) Allow 1 volume vs. multi-volume; Add slope options
25 Apr 2012, RW Cox, 3dNormalityTest, level 1 (MICRO), type 2 (NEW_OPT) Add -pval option, to get a 'pure' p-value out
24 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Can read .niml.tract files as DOs. Nothing too fancy yet Tractography files are loaded and handled like any DO. See function SUMA_DrawTractDO(). 24 Apr 2012, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT) Add censor stuff to 1dplot, for Colm
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) More I/T selector linkage modes. 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Show data value at crosshair directly in display See SUMA_UpdateCrossHairNodeLabelFieldForSO(), SUMA_FormNodeValFieldStrings(), and SUMA_UpdateNodeValField() 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Better handling on multiline centering for display in viewer window. 16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) New option to control which node-based DOs are displayed. See SUMA's interactive help on 'Ctrl+p' for details. 16 Apr 2012, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) Added -closest_possible For allowing the substitution of the projection result with the closest node that could be found along any direction. See changes to SUMA_GetM2M_NN() 16 Apr 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -do_draw_mask to restrict where node-based DOs are shown 16 Apr 2012, ZS Saad, 1dTsort, level 1 (MICRO), type 2 (NEW_OPT) Added -imode to return the mode of 1D file content. 16 Apr 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -regress_bandpass, for bandpass filtering via regression
05 Apr 2012, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add -zcount option: count number of zero values in a voxel
30 Mar 2012, RC Reynolds, @auto_tlrc, level 1 (MICRO), type 2 (NEW_OPT) added option -inweight Added for S Horovitz and S Tinaz.
22 Mar 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Improve display of node-based DOs. ctrl+p for showing subset of objects. Node-based DOs overwhelm the display. Ctrl+p allows one to show DOs only around the selected node, or just at it. See also DriveSuma's -do_mask_mode option. 22 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Add values at node to the display. This involved an improvement to the centering of text so that one can center each line in a paragraph 22 Mar 2012, ZS Saad, SurfaceMetrics, level 1 (MICRO), type 2 (NEW_OPT) Now outputs NIML dsets and Displayable objects for certain metrics
14 Mar 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -num_chan and -max_quiet_trs; default sleep = 1.1*TR, max of 2 Added for J Evans and V Roopchansingh.
12 Mar 2012, RC Reynolds, @SUMA_AlignToExperiment, level 1 (MICRO), type 2 (NEW_OPT) added -overwrite_resp, so that processing does not have to stop and wait Also, used 'find' grab *.nii, to fix the failure reported by R Ray. Forgot to put this in with the afni_proc.py change...
05 Mar 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT) Added option auto-completion for AFNI's programs for csh users The implementation of this feature is via apsearch. In particular, apsearch -update_all_afni_help now creates the necessary commands for csh's complete program to know about available options. See apsearch -help for details. This was done in conjunction with Brian Pittman.
01 Mar 2012, RW Cox, 1dBport, level 2 (MINOR), type 2 (NEW_OPT) Several things to keep Rick happy Option '-band fbot ftop' can now be used more than once. New option '-nozero' means to NOT include the 0 frequency. New option '-invert' means to calculate the frequency indexes to remove from the various '-band' options, then invert them to KEEP only those frequencies instead. That is, only the frequencies NOT specified via '-band' will be output in the resultant 1D file.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added option to use html viewer for WAMI results. This is to allow users to click on a URL if one is available for a certain atlas result. For now the display is very crude and only accessible with -DWEBBY_WAMI=YES. 29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added 'ctrl+W' that allows saving results from interactive correlations. This allows for convenient saving of interactively created datasets such as those from single-subject, or group correlation maps in resting state.
27 Feb 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allow on the fly definition of standard meshes with -i ld120, for example.
24 Feb 2012, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Options -val_diff and -sval_diff to compare values in 2 dsets. 24 Feb 2012, ZS Saad, 3dMEMA, level 2 (MINOR), type 2 (NEW_OPT) 3dMEMA can now handle surface-based data It makes use of the new I/O functions that use AFNI's C-library.
22 Feb 2012, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) Compute the mode of ROI voxels, see -mode and -nzmode 22 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -randomize_trs and -seed Affected 1d_tool.py, afni_util.py, lib_afni1D.py and lib_textdata.py.
21 Feb 2012, RW Cox, 3dAutobox, level 1 (MICRO), type 2 (NEW_OPT) Add -npad option, for Larry Frank 21 Feb 2012, DR Glen, whereami, level 4 (SUPER), type 2 (NEW_OPT) Web-based access atlases available Able to query web atlases from whereami and open webpages Support starting with rat brain atlas from Elsevier's BrainNavigator
16 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) more quick termination updates - added -max_images - do not init vol search state to 2, would limit volumes to 40 - include fl_start in no_wait test - look for new vol worth of images, but no volume match
10 Feb 2012, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -check_results_dir for Z Saad Also, changed -tcat_outlier_warn_limit to -tcat_preSS_warn_limit.
09 Feb 2012, ZS Saad, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT) Added -sdata, making 3dSurf2Vol compatible with multitude of surface dsets
07 Feb 2012, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT) Added -out option to handle output in various formats. Also added -func ALL option. 07 Feb 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -bkg_col and -autorecord options
06 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added automatic sub-brick selection matching IxT in interface Also see corresponding env var: SUMA_IxT_LinkMode
31 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_apply_ricor
23 Jan 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Allowed addition of 'R' or 'L' when jumping to a node. This make DriveSuma work well with node indices that are specified for two hemispheres as is done in the batch mode of 3dGroupInCorr. This applies to both suma and DriveSuma 23 Jan 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added -ld and -no_ld options @SUMA_Make_Spec_FS by default now runs MapIcosahedron at two ld values. 23 Jan 2012, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Added -atlas_followers Automatically bring along atlas datasets under -surf_anat's directory.
20 Jan 2012, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added -h_web, and -Vname= to all C command-line programs. See also apsearch -web_prog_help option
19 Jan 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Allow definition of DO on the fly with -fixed_do, -mobile_do. See DriveAfni -help and suma -help_nido
18 Jan 2012, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT) -s option to test string NI elements 18 Jan 2012, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 2 (NEW_OPT) -closest_* options to create find nodes that fall closest to XYZ locations
17 Jan 2012, ZS Saad, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Allowed BATCH mode to work on surfaces.
13 Jan 2012, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT) Options -pre and -app help in creating filenames regarding of type
11 Jan 2012, ZS Saad, 3drefit, level 1 (MICRO), type 2 (NEW_OPT) Added -copytables to copy label tables and atlas point lists
10 Jan 2012, ZS Saad, 3dTagalign, level 1 (MICRO), type 2 (NEW_OPT) Added interpolation options.
09 Jan 2012, ZS Saad, suma-general, level 1 (MICRO), type 2 (NEW_OPT) Added -setenv to all SUMA programs 09 Jan 2012, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -setSUMAenv,-N_fore_smooth, and -N_final_smooth
06 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT) Added -keep_separate to allow for another way to split ROIs
04 Jan 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Automatically add an Atlas to whereami list if encountered in the session 04 Jan 2012, ZS Saad, ROI2dataset, level 1 (MICRO), type 2 (NEW_OPT) Added -nodelist_with_ROIval to facilitate splitting ROIs 04 Jan 2012, ZS Saad, @Atlasize, level 1 (MICRO), type 2 (NEW_OPT) Allow for delimiters in keys file and handle names with spaces Similar additions are made to @MakeLabelTable
30 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Simplified how afni handles custom group or single-subject atlases By default, SessionAtlases and AFNI_SUPP_ATLAS_DIR/CustomAtlases.niml are added to the atlas list for whereami queries. 30 Dec 2011, ZS Saad, @MakeLabelTable, level 2 (MINOR), type 2 (NEW_OPT) Improved @MakeLabelTable's creation of ATLAS niml files 30 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Numerous new options to 3dinfo, including checks for dset presence on disk
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) SUMA now allows for direct recording to disk. See SUMA's ctrl+h for key ctrl+R for details. Related environment variable is SUMA_AutoRecordPrefix. 20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) SUMA now displays area labels in the viewer, F9 key toggles it See SUMA's ctrl+h output in the section for F9 Related environment variable is SUMA_ShowLabelsAtCrossHair. 20 Dec 2011, ZS Saad, 3dUpsample, level 2 (MINOR), type 2 (NEW_OPT) Allow for upsampling to go to 11 (actually 320) and control output datum
13 Dec 2011, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) -init_xform to allow for an initial transformation of -surf_anat 13 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) -same_* options return information about dset pairs
12 Dec 2011, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT) Small improvements and addition of logging option of search results See -apsearch_log_file option for details. Logging is only enabled if AFNI_LOG_BEST_PROG_OPTION is set to YES. 12 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Slice displays can now show atlas labels in addition to slice location The displays are turned on by right-clicking on the slice viewer's color bar and then setting the 'Label' to something other than 'OFF' See isqCR_getlabel, ISQ_getlabel, and AFNI_get_dset_val_label in code
07 Dec 2011, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Added atlas creation of aseg, aparc+aseg, in addition to aparc.a200* See whereami's example 3 for how to extract ROIs from FreeSurfer atlases.
06 Dec 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT) -stdin for input More tweaking of search distances and a battery of tests to help decide if tweak is in the right direction.
05 Dec 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) Added -h_view to all C command-line programs. See also apsearch -view_prog_help option
02 Dec 2011, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT) -XYZscale is added to scale the coordinates of a surface Surface that are not in mm coordinates can look pretty bad in SUMA. This scaling option can be used to easily change coordinates from cm to mm for example. 02 Dec 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Added 'Save' button to suma text info windows 02 Dec 2011, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) Add -ortvec option (to appease the Inati) Lets the pitiful user add multiple baseline (i.e., ort) vectors from a single file.
30 Nov 2011, ZS Saad, ConvertDset, level 1 (MICRO), type 2 (NEW_OPT) -pad_to_node 0 now padds output dset to max node in input dset
25 Nov 2011, ZS Saad, to3d, level 1 (MICRO), type 2 (NEW_OPT) Added -quit_on_err Keeps to3d from going in interactive mode in case of error. 25 Nov 2011, ZS Saad, Dimon, level 1 (MICRO), type 2 (NEW_OPT) Added -gert_quit_on_err Passes -quit_on_err option to to3d.
22 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -h_find as a global option afni -help now outputs information about 'Global options' 22 Nov 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) allow for passing variables directly, not via -svar
21 Nov 2011, ZS Saad, apsearch, level 1 (MICRO), type 2 (NEW_OPT) Added -all_opts to show all options for a program 21 Nov 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -all_opts as a global option The option is the equivalent of running apsearch -all_opts for a certain program.
17 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) If AFNI_NO_OPTION_HINT, don't bother with helpful suggestions
10 Nov 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 2 (NEW_OPT) Add ExtraSet option That is, to correlate seeds from the TimeSeries dataset with voxel data from the ExtraSet dataset. Ziad asked for something like this, so here it is.
09 Nov 2011, RW Cox, 3dUndump, level 2 (MINOR), type 2 (NEW_OPT) Add -ROImask option To put values into locations defined by a mask dataset.
07 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -blur_to_fwhm and -blur_opts_B2FW Added for E Nelson and J Jarcho.
03 Nov 2011, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 2 (NEW_OPT) added -prefix option; allow for 3dAllin failures; copy time info Updates by N Mei and A Messinger.
31 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_tr_stats and -warn_tr_stats options
26 Oct 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) Made SUMA hide overlay from SUMA whenever 'See Overlay' is off in AFNI
19 Oct 2011, RC Reynolds, @2dwarper.Allin, level 1 (MICRO), type 2 (NEW_OPT) added a -mask option Added for A Messinger.
18 Oct 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) Added -available_npb* options to suggest available port blocks 18 Oct 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) added blur size control; removed requirement of stim timing files
14 Oct 2011, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) now processes surface data - added 'surf' processing block, and corresponding '-surf_*' options: -surf_anat, -surf_spec, -surf_anat_aligned, -surf_anat_has_skull, -surf_A, -surf_B, -surf_blur_fwhm - compute errts and TSNR by default (had required option or blur est)
11 Oct 2011, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT) Added support for NIFTI datasets 11 Oct 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT) Added new options for extracting field values in scripts
04 Oct 2011, ZS Saad, GroupAna, level 2 (MINOR), type 2 (NEW_OPT) Added support for writing NIML files as output This also required writing a few new matlab functions such as BrikInfo_2_niml_writesimple. 04 Oct 2011, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT) Added -min_nodes option 04 Oct 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -anat_has_skull option
03 Oct 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -censor_infile (e.g. to remove TRs from motion params) Added for N Adleman.
21 Sep 2011, RW Cox, 3dTshift, level 1 (MICRO), type 2 (NEW_OPT) Add -voxshift option 21 Sep 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add -2sided option
13 Sep 2011, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT) Added non_zero and count options
06 Sep 2011, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) added -fast option, short for: -sleep_init 50 -sleep_vol 50
26 Aug 2011, RW Cox, 3dclust, level 1 (MICRO), type 2 (NEW_OPT) add -savemask option
09 Aug 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add '-cvarinv' option for Vinai
03 Aug 2011, RC Reynolds, align_epi_anat.py, level 1 (MICRO), type 2 (NEW_OPT) added -save_orig_skullstrip, to avoid oblique transforms This was added for afni_proc.py.
02 Aug 2011, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT) Add '-inmask' option, to use internal mask To be compatible with AFNI's Clusterize GUI, which was also modified to output this option when appropriate.
20 Jul 2011, ZS Saad, 1dcat, level 1 (MICRO), type 2 (NEW_OPT) added -sel option to 1dcat with -sel one can apply the same selection of columns and rows to all files on the command line, allowing the use of wildcards when specifying input 1D files.
15 Jul 2011, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT) Add -center option for covariates (cf. Chen Gang)
14 Jul 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_max_displace, for maximum motion displacement
13 Jul 2011, RC Reynolds, gen_group_command.py, level 1 (MICRO), type 2 (NEW_OPT) added -exit0 and babbled about possible artifact tests
05 Jul 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) add -NOLINE to include clipping of points outside the box
27 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) added -dset_index0_list/-dset_index1_list options, etc. - ttest++ and MEMA commands now apply directories to datasets - changed Subject.atrs to be VarsObject instance, not dictionary
24 Jun 2011, ZS Saad, afni-general, level 1 (MICRO), type 2 (NEW_OPT) added global option -pif which is used to flag certain commands. -pif PROCESS_ID_FLAG is used to flag a particular AFNI command so that you can identify from the shell that command's process id by grepping for PROCESS_ID_FLAG on the output of 'ps -a'.
20 Jun 2011, ZS Saad, 3drename, level 1 (MICRO), type 2 (NEW_OPT) added support for -overwrite 20 Jun 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added eta2 function (alongside '3ddot -doeta2')
16 Jun 2011, ZS Saad, 3dSurfMask, level 3 (MAJOR), type 2 (NEW_OPT) Major improvements for mask creation and voxel distance computations Option -fill_method SLOW produces more accurate masks for voxels inside the closed surface. In addition, the program outputs a dataset with the shortest distance of each voxel to the surface. See examples under 3dSurfMask -help. 16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT) -flip_orientation allows for reversing triangle orientation. See new examples under SurfPatch -help 16 Jun 2011, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT) added -doeta2 via new THD_eta_squared_masked Added for Shinchan.
15 Jun 2011, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT) Add -sum option; rearrange -help output a little.
08 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT) Added -npb and modified title bar to reflect bloc of ports You can have multiple instances of programs talking to each other. See afni's help for details on the -npb option.
07 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT) Allow multiple instances of communicating programs per machine. This was done by generalizing option -np PORT_OFFSET which allows users to use a different set of ports for different AFNI/SUMA/etc. sessions.Port numbers should no longer be hard coded anywhere. New dedicat ed ports should be added to then new init_ports_list() function. 07 Jun 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added 'w' key for writing out colormap to disk. See suma's help for the colormap. (press ctrl+h with cursor over the colormap in the surface controller) 07 Jun 2011, ZS Saad, suma, level 1 (MICRO), type 2 (NEW_OPT) -np, -list_ports, -port_number* control and report port assignments See suma -help for details. 07 Jun 2011, ZS Saad, afni, level 1 (MICRO), type 2 (NEW_OPT) -list_ports, -port_number* give port assignment information See afni -help for details.
03 Jun 2011, RC Reynolds, Makefile, level 2 (MINOR), type 2 (NEW_OPT) removed -lpng from Makefile.macosx_10.6_Intel_64 We added -lpng because we were compiling our own OpenMotif (configure option?), but fink's version does not need it. 03 Jun 2011, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -volreg_compute_tsnr/-regress_compute_tsnr Volreg TSNR is no longer the default, but regress TSNR is.
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) compute TSNR datasets (added -compute_tsnr); added -regress_make_cbucket 02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) de-meaned motion regressors is now the default - added -regress_apply_mot_types to specify motion types for regression - added -regress_no_motion_demean and -regress_no_motion_deriv - by default, demean and deriv motion parameters are created - by default, demean motion parameters are applied in the regression (replacing the original 'basic' parameters, which should have no change in betas of interest, just the constant polort betas)
27 May 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -split_into_pad_runs (for regress motion per run)
25 May 2011, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add -tdiff option == statistics on first differences of data 25 May 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -global_to_local and -local_to_global for G Chen
24 May 2011, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add -noline and -box options To plot markers at each point, without or with lines connecting them.
20 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 2 (NEW_OPT) Add normal theory CI for Pearson; Add -block option Pearson correlation (the default) now gets the normal theory confidence interval printed at no extra charge. To allow for serial correlation, the -block option enables random length block resampling bootstrap. Add some more help text to explicate things a little better.
19 May 2011, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT) Added support for multiple reference time series. Search for -var* options in @RetinoProc -help. 19 May 2011, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 2 (NEW_OPT) Added option to use best of multiple reference time series. Search for -multi_ref_ts in 3dRetinoPhase -help
18 May 2011, ZS Saad, @RetinoProc, level 3 (MAJOR), type 2 (NEW_OPT) Added options for mapping to specific layers, and the use of delay The options -wm, -pial, etc. allow for tight control of mapping onto specific layers in the cortex. Option -delay improves latency estimation compare to using the phase of the fundamental frequency. 18 May 2011, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 2 (NEW_OPT) Added options to 3dRetinoPhase to estimate latency as in 3ddelay The two options for computing delays, instead of phase, are -phase_estimate DELAY, and -ref_ts REF_TS . See program's -help for details. Also added -ort_adjust which is needed to account for lost DOF in external detrending when estimating the significance of correlation coefficients with delay estimation. The program now output a correlation coefficient with the visual field angles datasets. And speaking of correlation coefficients, the significance levels should be taken with a grain of salt, especially in derived datasets such as field angle, and VFR in SurfRetinoMap. 18 May 2011, ZS Saad, 3ddelay, level 2 (MINOR), type 2 (NEW_OPT) Added options to 3ddelay to improve its utility for retinotopy analysis The new options are -phzreverse and -phzscale. Though useful, you are better off using 3dRetinoPhase -phase_estimate DELAY option. It is much more convenient for retinotopy analysis and fits better in @RetinoProc
28 Apr 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT) reconcile LUS.py with LS.py in prep for uber_align_test.py 28 Apr 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -align_epi_strip_method
15 Apr 2011, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT) added -slice_times and -slice_times_verb, to show siemens slice timing
13 Apr 2011, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT) added FROM_IMAGE timing pattern (for Siemens mosaic images)
08 Apr 2011, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Added options -reduce* to compute results on reduced grid This would help in speeding up the computing of stats over large regions without paying too high a premium on processor time. Changes were made in 3dLocalstat.c and mri_nstats.c. Micro modification in r_new_resam.c's r_new_resam_dset.
05 Apr 2011, RC Reynolds, python_module_test.py, level 1 (MICRO), type 2 (NEW_OPT) added PyQt4 to test list
29 Mar 2011, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add -OKsmallmask option To let deranged users take their statistical fortunes into their own hands.
22 Mar 2011, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT) -roi_mask allows creation of separate histogram for each ROI in mask. 22 Mar 2011, RW Cox, 3dTfitter, level 1 (MICRO), type 2 (NEW_OPT) Add -l2sqrtlasso option Yet another solution method, this time with SQRT(LASSO) penalty.
11 Mar 2011, RW Cox, 3dTfitter, level 1 (MICRO), type 2 (NEW_OPT) Add L2+LASSO regression option Mostly for experimentation at this moment in time.
07 Feb 2011, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Added -batch mode of operation To appease the Lebanese and Italian masses.
27 Jan 2011, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT) Add -sendall option, to palliate the Texan hordes.
13 Jan 2011, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -gert_write_as_nifti and -gert_create_dataset requested by V Roopchansingh
03 Jan 2011, ZS Saad, 3dUniformize, level 2 (MINOR), type 2 (NEW_OPT) Changed 3dUniformize to accept byte, short, or float input. These changes also avoid data clipping that was necessary when output data was handled as shorts. The output format is similar to that of the input. -auto_clip is now the default.
27 Dec 2010, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT) -maxwait option limits amount of time waiting for AFNI Instead of old fixed value of 9 s. Also, if program can't connect to AFNI at all, exit status will be 1. This feature can be used in a script to check if AFNI is running with plugouts enabled, and if not, then start a copy.
23 Dec 2010, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT) added -use_old_mosaic_code This is phase 1 of dealing with Siemens mosaic format in Dimon. Siemens mosaic functions we moved to new mri_process_siemens.c, with the ability to use the old code preserved with this option.
10 Dec 2010, ZS Saad, 3BrickStat, level 2 (MINOR), type 2 (NEW_OPT) Added -mrange and -mvalue options to 3dBrickStat
09 Dec 2010, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT) Made 3dhistog output NIML 1D format with -prefix option With -prefix's output users can get properly labeled output with a simple command like 1dRplot -input hist.1D
30 Nov 2010, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added option -final_sort_by_prog
22 Nov 2010, ZS Saad, 3dRowFillin, level 2 (MINOR), type 2 (NEW_OPT) Added XYZ.OR, and XYZ.AND to 3dRowFillin
19 Nov 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -write_all_rest_times, moved write_to_timing_file to afni_util.py option added for J Poore
16 Nov 2010, ZS Saad, ExamineXmat, level 2 (MINOR), type 2 (NEW_OPT) A major rewrite of ExamineXmat see ExamineXmat -help for details 16 Nov 2010, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT) Add cubic, quintic, and heptic polynomial warps.
10 Nov 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) Add -rankize and -no1sam options
08 Nov 2010, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 2 (NEW_OPT) can now generate 3dttest++ commands
05 Nov 2010, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT) Added -attribute, -match, and -f options to niccc See niccc -help for details. 05 Nov 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) New -BminusA option This is Ziad's fault (again).
04 Nov 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added regress_basis_multi, -regress_no_ideal_sum One can specify either one basis function or one per stim_times file.
01 Nov 2010, RW Cox, 3dTstat, level 1 (MICRO), type 2 (NEW_OPT) Add -centromean statistic to the mix 01 Nov 2010, RW Cox, 3dClipLevel, level 1 (MICRO), type 2 (NEW_OPT) Add -doall option
29 Oct 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_indices_baseline, _motion and _interest
28 Oct 2010, ZS Saad, 3dcopy, level 1 (MICRO), type 2 (NEW_OPT) Support for -overwrite
27 Oct 2010, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT) added -show_bad_char and -show_bad_all
26 Oct 2010, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT) solidified 3dMEMA commands This is now used to generate AFNI_data6/group_results/s4.3dMEMA.V-A.
22 Oct 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added NodeMarker field to the spec file The NodeMarker is a NIDO object that gets replicated at all nodes. Replicated markers inherit the color of the nodes IF the NodeMarker has no color attribute. 22 Oct 2010, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added -RenderMode option to control how a surface is rendered This option is the same as Surface Controller-->RenderMode menu 22 Oct 2010, ZS Saad, ConvexHull, level 2 (MINOR), type 2 (NEW_OPT) Added -q_opt option to allow for delaunay triangulation of 2D coordinates This new option makes it easy to create a surface from a set of ECOG electrodes.
21 Oct 2010, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -shift_to_run_offset
20 Oct 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -tcat_remove_last_trs, -ricor_regs_rm_nlast Added for J Czarapata. 20 Oct 2010, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -sort_by_acq_time for -dicom_org on Philips data Added for Manjula.
15 Oct 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -multi_timing_to_events, -multi_timing_to_event_pair, -per_run - Modified timing_tool.py, lib_timing.py, lib_textdata.py, afni_util.py. - Added for N Adleman.
14 Oct 2010, RW Cox, afni InstaCorr, level 1 (MICRO), type 2 (NEW_OPT) Add Despike option
08 Oct 2010, RW Cox, 3dBandpass, level 1 (MICRO), type 2 (NEW_OPT) Add -despike option to program.
07 Oct 2010, DR Glen, Plugout commands, level 2 (MINOR), type 2 (NEW_OPT) Commands to get current RAI xyz or IJK coordinates in a plugout script
06 Oct 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT) Add -zskip option Lets users skip the processing of voxel values that are exactly zero -- to allow for non-overlap between subjects.
27 Sep 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Began code changes to allow for volume rendering Changes mostly involve SUMA_volume_render.c and were made with Joachim Bottger's help. Of note is the additionof the Volume Obj ect structure SUMA_VolumeObject.
18 Sep 2010, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -Dsp option to allow control of Dset display mode
03 Sep 2010, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Script now process v1.label files from FreeSurfer The output is two datasets per hemisphere, one for the ??.v1.prob.label and one for the ??.v1.predict.label.
25 Aug 2010, ZS Saad, ConvertDset, level 1 (MICRO), type 2 (NEW_OPT) Added -no_history option
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Shift+Ctrl left, right rotates surface about Z axis Useful for rotating flat surfaces
18 Aug 2010, RC Reynolds, @build_afni_Xlib, level 1 (MICRO), type 2 (NEW_OPT) added -lib32 for building 32-bit on a 64-bit Linux box
17 Aug 2010, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) allowed married timing files Also, delete output script on failure (have -keep_script_on_err option).
09 Aug 2010, ZS Saad, suma-general, level 1 (MICRO), type 2 (NEW_OPT) Allows reading 5-column colormaps
04 Aug 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_CS_NN, default to 123 Also, changed -niml to -both so that 1D files are output, and changed the prefix to ClustSim (from rm.CS) so those files are not deleted. If ClustSim is explicitly requested, require blur estimation.
02 Aug 2010, RW Cox, 3dGroupInCorr, level 1 (MICRO), type 2 (NEW_OPT) Add -np option to change NIML port used to talk to AFNI Per the request of Andreas Hahn. 02 Aug 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) check that stim_file/_time files match datasets, and that dsets exist - default is to check that files are appropriate for the input data - default is to check that input datasets exist - added options -test_stim_files and -test_for_dsets - afni_proc.py now depends on lib_afni1D 02 Aug 2010, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) small looks_like text change and remove TR from look_like_1D
30 Jul 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added options to evaluate whether a file is valid as 1D or stim_times Added -looks_like_1D, -looks_like_local_times, -looks_like_global_times and -looks_like_test_all. The main purpose is to have tests that afni_proc.py can apply.
28 Jul 2010, ZS Saad, plugout_drive, level 2 (MINOR), type 2 (NEW_OPT) Added SET_INDEX to plugout_drive
23 Jul 2010, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT) Add TENTzero and CSPLINzero response models To allow the HRF to be required to be zero at the start and stop times (i.e., it will be continuous, not suddenly drop off to zero).
22 Jul 2010, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add -both option (get NIML and 1D output in one run) 22 Jul 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options -regress_run_clustsim and -regress_opts_CS This is to apply 3dClustSim results for multiple comparison correction to the stats dataset output from 3dDeconvolve.
20 Jul 2010, RW Cox, 3dAutoTcorrelate, level 1 (MICRO), type 2 (NEW_OPT) -mmap option -- output large .BRIK file in a faster way
19 Jul 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -check_afni_version and -requires_afni_version This will allow the processing script to verify that the AFNI version is recent enough for the enclosed commands. 19 Jul 2010, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added -check_date, to verify whether the distribution is current 19 Jul 2010, RC Reynolds, @DriveAfni, level 1 (MICRO), type 2 (NEW_OPT) added -help
16 Jul 2010, RC Reynolds, 3dMean, level 2 (MINOR), type 2 (NEW_OPT) added -mask_union and -mask_inter, for creation of mask datasets
15 Jul 2010, RW Cox, 3dREMLfit+3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) Add -STATmask option Allows user to specify mask for FDR calculations, when no -mask is used.
12 Jul 2010, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) add MION to the -stim_times HRF repertoire Now will they stop bugging me?! (of course not) 12 Jul 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -truncate_times and -round_times for S Durgerian
08 Jul 2010, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Add -NN option (clustering method) and -prefix (output filename)
07 Jul 2010, RW Cox, 3dClustSim, level 1 (MICRO), type 2 (NEW_OPT) Added info to output header; also, added -niml option
01 Jul 2010, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) Added -mapfile option, allowing SurfToSurf to reuse an existing mapping.
28 Jun 2010, RC Reynolds, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT) added -eta2 (Cohen eta squared) for HJ Jo Also added -mask and -mask_only_targets.
22 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) 3dToutcount detrending now defaults to Legendre polynomials Using Legendre polynomials, 3dToutcount polort can exceed 3 (limit noted by I Mukai and K Bahadur). Added options -outlier_legendre and -outlier_polort. 22 Jun 2010, RC Reynolds, 3dToutcount, level 2 (MINOR), type 2 (NEW_OPT) added -legendre option, which also allows polort > 3
08 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_censor_outliers and -regress_skip_first_outliers 08 Jun 2010, DR Glen, RetroTS.m, level 2 (MINOR), type 2 (NEW_OPT) Allowed for alt+z2 slice timing
04 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) moved outlier counting outside of tshift block - if only one regressor, use 1dcat for 'sum' ideal - added -count_outliers, default to 'yes' - outlier counting is now at end of tcat block 04 Jun 2010, RC Reynolds, 3dToutcount, level 1 (MICRO), type 2 (NEW_OPT) added -fraction to output fraction of bad voxels, instead of count This will be used by afni_proc.py for censoring.
25 May 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added click and drag for third mouse button
21 May 2010, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT) Added -dset option to take in niml dsets
18 May 2010, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT) New option -vthr, to set threshold for ignoring regression vectors In the olden version, vectors whose L1 norm was less than 0.000333 times the largest vector's L1 norm were cast out before the analysis -- this was to fix a problem of Rasmus Birn's. However, some people whose initials are HJJ want to use LHS vectors whose magnitude varies a lot. So now the user has to specify the 'cast out' vector threshold with the -vthr option, whose default is NOT 0.000333 but is 0.0 -- that is, only exactly zero vectors will be unused by default.
12 May 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_censor_first_trs for A Barbey This is needed when also using -regress_censor_motion. 12 May 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -censor_first_trs, to mix with -censor_motion results
04 May 2010, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) Added -nzsigma to 3dROIstats 04 May 2010, ZS Saad, 1dtranspose, level 1 (MICRO), type 2 (NEW_OPT) Allowed 1dtranspose to accept -overwrite The main reason for this is to allow such a command: 1dtranspose -overwrite FILE.1D FILE.1D without having to create temporary files.
01 May 2010, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added -max_consec for Liat of Cornell
29 Apr 2010, RW Cox, InstaCorr, level 1 (MICRO), type 2 (NEW_OPT) Add Kendall Tau_b to the correlation menu For fun, and as a start towards something else. 29 Apr 2010, RW Cox, 3dTcorrelate, level 1 (MICRO), type 2 (NEW_OPT) add -ktaub option
26 Apr 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_opts_reml
16 Apr 2010, ZS Saad, 3dbucket, level 2 (MINOR), type 2 (NEW_OPT) -agluto option = amalgamated -prefix and -glueto
24 Mar 2010, RW Cox, 3dFWHMx, level 1 (MICRO), type 2 (NEW_OPT) Add -2difMAD option, for dealing with PET data, maybe.
23 Mar 2010, ZS Saad, 1dplot, level 2 (MINOR), type 2 (NEW_OPT) Added -jpgs, and -pngs to allow easier size setup. 23 Mar 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_compute_fitts option, to save memory in 3dDeconvolve
19 Mar 2010, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT) Added option to calculate Euclidian distance
16 Mar 2010, ZS Saad, 3dcalc, level 2 (MINOR), type 2 (NEW_OPT) -within option to test Min <= X <= Max
09 Mar 2010, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) -nomeanout to get rid of mean in output
05 Mar 2010, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Added -stat P2skew to calculate Pearson's second skewness coefficient
03 Mar 2010, ZS Saad, 3dmerge, level 2 (MINOR), type 2 (NEW_OPT) -isomerge and -isovalue options that mimick 3dclust's options 03 Mar 2010, ZS Saad, 3dmerge, level 2 (MINOR), type 2 (NEW_OPT) -1clust_depth option to determine how deep voxel is in cluster 03 Mar 2010, ZS Saad, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT) -depth option to determine how deep voxel is in mask
01 Mar 2010, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT) Added -FSversoin, -hemi, and -FScmap* options for 2009 parcellations 01 Mar 2010, ZS Saad, @FS_roi_label, level 2 (MINOR), type 2 (NEW_OPT) Modified -name to accept 'ALL' 01 Mar 2010, RW Cox, InstaCorr, level 1 (MICRO), type 2 (NEW_OPT) Add Spearman and Quadrant correlation options
26 Feb 2010, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT) -labeltable option to add a label table to a dataset
24 Feb 2010, RW Cox, 3dAllineate, level 2 (MINOR), type 2 (NEW_OPT) New cost functional -lpc+ Combination of lpc + hel + crA + nmi + mi. Also some micro changes to allow more -twobest starting points and the like.
20 Feb 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -timing_to_1D, -tr and -min_frac for PPI scripting (and B Benson)
15 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) -arg*1 options to keep from getting 0 in arg* output 15 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) -*mask options to allow masking
12 Feb 2010, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT) -*_cut_surfaces to deal with bad triangles on standard flat surfaces 12 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) Added -argmin1, -argmax1, -argabsmax1 options to increment argument by 1
28 Jan 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) Options for multiple cost functionals,edge control multi_cost option for trying out different cost functionals. check_cost option for comparing for big differences among cost functionals edge_erodelevel option for adjusting the number of layers to erode for edge option
21 Jan 2010, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -tlrc_opts_at; made tiny mod to scaling operation
15 Jan 2010, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -regress_fout yes/no option for G. Pagnoni
14 Jan 2010, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Added -rank and -frank options to 3dLocalstat
24 Dec 2009, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -approx_gifti option
15 Dec 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Allow label based sub-brick selection in AFNI and SUMA
25 Nov 2009, ZS Saad, MapIcosahedron, level 3 (MAJOR), type 2 (NEW_OPT) Added -NN_dset_map and -dset_map options to map dsets onto new meshes The program now automatically warps LabelDsets specified in the spec file, or any dataset specified on the command line.
24 Nov 2009, ZS Saad, 1dmatcalc, level 2 (MINOR), type 2 (NEW_OPT) Added &read4x4Xform to read in spatial affine transformations. 1dmatcalc can now take in spatial affine transforms in vector or matrix form
23 Nov 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT) Add -bpass option 23 Nov 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT) Add various options in the last few days * -seed = a different dataset for the seed time series * -bpass = instead of -polort * -Gblur = blurring * -Mseed = extra smoothing around the seed * -Hist = output the histogram of the correlations
20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT) apply_prefix option to save automasked input avoids 3dcalc step that is usually used to apply an automask.
17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT) SUMA now handles labeled datatets in a special manner An example of a labeled dataset would be FreeSurfer's annotation files. If an annotation file is present in the spec file (@SUMA_Make_Spec_FS), SUMA will display it as part of the background. You can chose to display the labeled dataset in color, contours, or both. Data from labeled datasets is now shown under the 'Lbl' field in the surface controller's Xhair block. 17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT) Option -label_dset creates a labeled dataset from ROIs. Labeled datasets are now rendered in a special manner in SUMA 17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT) Option -dset creates a labeled dataset from annotation file. Labeled datasets are now rendered in a special manner in SUMA 17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) Script now automatically sets up the spec file with labeled datasets Labeled datasets are created from annotation files, and are now rendered in a special manner in SUMA
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT) Added options to check for, and correct 'bowties' in pathches. Bowties in patches result in non 2-manifold stiched surfaces whose volume cannot be caluclated. The *bowtie option deal with such cases. 09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT) Added options to shrink patch contours at nodes not in selected nodes. See options -adjust_contour for details. 09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT) Added option for improved node volume estimation. The new measure, called node_volg, uses Gauss' Theorem to estimate the volume associated with a node in two isotopic surfaces. This option is more robust to surface curvature variations.
04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT) 3dAllineate option for motion correction volreg_method allows 3dAllineate, which is useful for DTI data. Bug fix for post-transformation matrix and dataset view
23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -censor_fill and -censor_fill_par These options are to zero-pad TRs that were censored by 3dDeconvolve.
19 Oct 2009, RW Cox, 3dBlurInMask, level 1 (MICRO), type 2 (NEW_OPT) add -preserve option, to keep Rick Reynolds from defecting to SPM 19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options for using 3dBlurInMask, instead of 3dmerge - added -blur_in_mask, -blur_in_automask and -blur_opts_BIM - added -sep_char and -subj_curly 19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT) New master options, dset1/2 terminology New master_nnn_dxyz options to specify output resolution dset1 and dset2 for non-EPI/anat alignment with lpa cost function and turns off preprocessing steps giant_move option turns off resampling and changes master options Expanded help - including fuller description of edge method Removed volume registration (motion correction) for anat2epi option by default. AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output depending on BASE, SOURCE or external dataset names for all output
16 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -demean, to demean motion parameters, for example The polort 0 values should be more accurate baseline constants. Useful for creating a proper polort baseline w/3dSynthesize.
13 Oct 2009, ZS Saad, quickspec, level 1 (MICRO), type 2 (NEW_OPT) -tsnad to allow for setting anatomical flag and local domain parent 13 Oct 2009, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT) -xmat_1D allows for single row transform definition
07 Oct 2009, ZS Saad, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) 1dplot's window frame now shows a title. See 1dplot -wintitle for details. 07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT) Add -Mmask option to allow multiple mask values For independent blurring (e.g., blur WM and GM separately).
06 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -set_run_lengths option, for varying run lengths Added for motion censoring and run padding.
29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT) Flexible slice timing options SliceOrder option allows for standard slice timing order alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input 29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT) Opt options available to compiled version All options available through the Opt structure are now available even with the compiled version of McRetroTS, making the compiled version functionally equivalent to the RetroTS.m version
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Improved the 'star' blurring interface.
18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT) Added option -n minnodes 18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT) Allow specifying external FreeSurfer color table.
16 Sep 2009, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -scale_data for J Meltzer
14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT) Allow specifying rmm in number of edges connecting nodes.
09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT) Allow @fast_roi to accept existing TLRC transformed anatomy 09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT) Add 'ball' options for mask generation 09 Sep 2009, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT) Add box and ball options to this program, per Kyle Simmons
04 Sep 2009, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT) if wget fails, try curl; added -curl and -testing options
27 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -regress_local_times, -regress_global_times Since the -local_times and -global_times options in 3dDeconvolve must be processed before the stimuli they refer to, it does nothing to pass them via -regress_opts_3dD. Hence, the options are needed.
24 Aug 2009, RW Cox, 3dAFNItoNIML, level 1 (MICRO), type 2 (NEW_OPT) Add -ascii option == way to dump dataset in plain text
21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_censor_motion and -regress_censor_prev Motivated by L Thomas and B Bones. 21 Aug 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT) added -show_censor_count
20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added motion censoring options Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask, -set_tr, -write_censor and -write_CENSORTR. Also modified afni_util.py, lib_afni1D.py and option_list.py.
14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -align_epi_ext_dset, to align anat to external EPI This may be important for multi-channel coil EPI data with low internal structural contrast. Users might align to the first (pre-steady-state) TR, even though that volume is not used in the analysis.
13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -volreg_tlrc_adwarp, to apply a manual Talairach transformation
27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) added -slibase_sm, for slice-major ordering of regressors RetroTS and afni_proc.py were incorrectly using this ordering. ** Analysis done prior to this probably needs to be re-done. 27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_labels and -show_label_ordering
23 Jul 2009, RW Cox, 3dTfitter, level 1 (MICRO), type 2 (NEW_OPT) Added -errsum option, to save error sums per voxel. And a -help example showing how the error sum of squares can be used to compute partial correlation coefficients of a fit. 23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -partition option 23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT) Single and Dual exponential models New models for 3dNLfim that use single and dual exponential models that are appropriate for MEMRI (Manganese Enhanced MRI
16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT) Added option to force autoscale on the graphing window The option is accessible by pressing 'A' in the graph window or under 'Graph->Opt->Scale->AUTO'.
14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added -max_rest, to limit the maximum duration of rest periods
23 Jun 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT) Add -Pmean option, based on poster I saw at HBM.
17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) version 2.0 : call e2a alignment and warp to standard space ready - mask warped EPI by its extents (at volreg step) - added -volreg_no_extent_mask, to block this masking - added 'extents' to list of mask in -mask_apply - change block dividers to more visual '===' with block names 17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added -make_3dd_contrasts and used general accuracy in block durations
16 Jun 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add '-ytran' option Apply an expression to the time series, to transform it prior to plotting. To elide the use of 1deval.
11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added masking abilities - in mask block, try to create anat and group masks - added -mask_apply option, for choosing mask to apply to regression - added -align_opts_aea, for extra opts to align_epi_anat.py
08 Jun 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT) added -despike_mask, fixed missing block warning, reordered terminal opts
29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -execute and now fail if block options have no corresponding blocks
27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) updates for alignment/warp/varying run lengths - added -volreg_warp_dxyz option - if align a2e, add -no_ss to @auto_tlrc - for varying run lengths, fixed application of '-volreg_align_to last' and the -regress_est_blur_* options (blur estimation loops were modified for this) - warping to new grid truncates to 2 significant bits (if < 2 mm)
21 May 2009, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT) Now output a grayscale 1D version of an image That is done by adding a .1D to the -prefix parameter. 21 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added 'align' processing block and -volreg_align_e2a option
19 May 2009, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT) Added -zerofill and -roisel options Added options to force output for empty ROIs. 19 May 2009, ZS Saad, 1ddot, level 2 (MINOR), type 2 (NEW_OPT) Added -okzero to keep program from exiting with all zero input Added options to force output for empty ROIs. 19 May 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Modified time out for DriveSuma to 5 minutes Time out can be controlled by environment variable SUMA_DriveSumaMaxWait
15 May 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) added -volreg_tlrc_warp option: can warp to standard space at volreg step 15 May 2009, RC Reynolds, afni_util, level 1 (MICRO), type 2 (NEW_OPT) added get_truncated_grid_dim
08 May 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT) The script now automatically turns FS annot files to SUMA ROI files
06 May 2009, RW Cox, afni, level 3 (MAJOR), type 2 (NEW_OPT) First edition of InstaCorr! Rough around the edges, but gnarly-ific to the level of the first inaccessible cardinal!
30 Apr 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 2 (NEW_OPT) return a node v2s time series when afni changes xhair position
29 Apr 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT) -nodelist* options to output node sequence forming ROI 29 Apr 2009, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT) -node_select_1D now respects node ordering 29 Apr 2009, ZS Saad, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT) -VarThresh* options for obtaining counts at different thresholds
28 Apr 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT) Add duration argument to SPMGx basis functions for deconvolution. For Tracy Doty, apparently.
15 Apr 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT) Add -thick option Plus: modify plot_ts.c to thicken the lines used for plotting the labels (so the fancy characters are filled in a little).
14 Apr 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 2 (NEW_OPT) added sample nifticlib program: clib_01_read_write.c
11 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -volreg_regress_per_run This is to apply the motion parameters of each run as separate regressors. 11 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -derivative and -set_nruns, fixed -show_cormat_warnings typo 11 Apr 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT) enhanced special option processing - added check_special_opts(), to be called before any processing - renamed -verbose_opts to -optlist_verbose - added -optlist_no_show_count 11 Apr 2009, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT) added calls to opts.check_special_opts() in 7 more python programs: gen_epi_review.py, make_random_timing.py, make_stim_times.py neuro_deconvolve.py, python_module_test.py, timing_tool.py, ui_xmat.py
10 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT) added -use_last_elem option for setting DICOM elements Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable. 10 Apr 2009, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -use_last_elem option for setting DICOM elements
09 Apr 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT) 'official' release with RETROICOR processing block: ricor o added 'across-runs' ricor_regress_method o added ricor information and usage to help (see 'RETROICOR NOTE') o maintain unscaled shorts if they are input o added -ricor_datum 09 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_cormat_warnings and -cormat_cutoff
08 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_rows_cols option
06 Apr 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added support for '.', ',', and space keys, and 'shw_0' 06 Apr 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT) Modify to allow output of more than 1 singular vector. Also, make the help more helpful. 06 Apr 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 2 (NEW_OPT) Add -vproj option To project central voxel onto low-dimensional local SVD space.
02 Apr 2009, RW Cox, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT) Add -Thresh option To save a count of how many other voxels are above threshold correlated with each seed voxel.
01 Apr 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Arrow keys based navigation along surface. See 'Alt+U-D' section in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added 'on the fly' dot product computation This feature is only available with SUMA's -dev option. It is still in testing mode and its interface may change. If intrigued, see 'D' key's help in SUMA's interactive usage help. 31 Mar 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added support for '[' and ']' keys and -view_surf 31 Mar 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -pad_to_many_runs, -reverse 31 Mar 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT) added global -verbose_opts option 31 Mar 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added get_typed_dset_attr_list, enhanced decode_1D_ints
26 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) Support for reading/writing MNI .obj surfaces
25 Mar 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Add -nobout option, to suppress baseline betas from -Rbeta/-Obeta. Per the request of Michael S Beauchamp, University of Texas.
19 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 2 (NEW_OPT) added -verbose_opts option, for being verbose during option processing 19 Mar 2009, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) a few additions and changes - allow container chars (e.g. []) in decode_1D_ints() - added is_valid_int_list() - changed str vars to istr (as str is a keyword)
18 Mar 2009, DR Glen, 3dZcat, 3daxialize, level 2 (MINOR), type 2 (NEW_OPT) NIFTI support Fixed support for NIFTI output in 3dZcat and 3daxialize Added -frugal option to 3daxialize to keep old behavior for AFNI format datasets. Existing -frugal option in 3dZcat imposes 'oldish' behavior too.
12 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT) SUMA talks to matlab. 12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_reml_exec and -regress_3dD_stop One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each.
11 Mar 2009, RW Cox, 3dANOVA, level 2 (MINOR), type 2 (NEW_OPT) Add -mask option to 3dANOVA, 3dANOVA2, 3dANOVA3
10 Mar 2009, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT) Sum option Sum option (for functional weighting of interiorosity measure)
09 Mar 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT) Add SPMG1 to -stim_times repertoire, and update help. 09 Mar 2009, RC Reynolds, suma, level 1 (MICRO), type 2 (NEW_OPT) added -motif_ver option
06 Mar 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT) Add 'WAV' function (from waver) to -stim_times repertoire.
05 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT) change -noinstall option to -localinstall
04 Mar 2009, RC Reynolds, afni, level 1 (MICRO), type 2 (NEW_OPT) added -motif_ver option 04 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT) added -noinstall option
10 Feb 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT) Added -anim_dup to slow down movies
02 Feb 2009, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT) SurfDist now outputs distances from one node to a set of other nodes 02 Feb 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) Added load_col option to DriveSuma
05 Jan 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT) Program no longer confined to FreeSurfer surfaces The program now allows the user to specify any morph sphere, not just sphere.reg or sphere. This required rewriting much of of the program's main section but the algorithm for the mapping remains unchanged. 05 Jan 2009, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT) Program uses new Spec writing function and writes different surface formats
10 Dec 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added new options for extra stimuli, RONI and an external volreg base - allow NIfTI datasets as input (but process as AFNI) - added -regress_extra_stim_files and -regress_extra_stim_labels - added -regress_RONI and -volreg_base_dset (for Jill Weisberg)
09 Dec 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT) Added -cm option to allow centering based on the center of mass
04 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT) Extend -stim_times_AM2 option to allow multiple amplitudes
24 Nov 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added options -infile_list and -show_sorted_list The -show_sorted_list option will print a list of files by run/index.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added Options menu, Show Cosmat and GUI help This is the initial release version, 1.0. 21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -test_libs option 21 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT) removed 'R' from basic test list, and applied verb 2 to base usage
20 Nov 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) incorporated real-time volume writing from V. Roopchansingh of MCW
18 Nov 2008, RW Cox, 3dANOVA programs, level 2 (MINOR), type 2 (NEW_OPT) Add option to output float-valued datasets. Set the AFNI_FLOATIZE environment variable to YES, and the output of 3dANOVA, 3dANOVA2, and 3dANOVA3 will be stored in float format instead of in scaled short format. [Per the request of Paul Hamilton] 18 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT) added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff also added the main help
13 Nov 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Added a NIDO sphere as Displayable Object See suma -help_nido for details. 13 Nov 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Added -al option to use 3dAllineate -lpa
06 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT) pre-release updates: - added many initial command-line options - added plot_xmat_as_one toggle button - added computation of cosine matrix and cosmat_warnings - separated GUI code into new file gui_xmat.py 06 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT) added option -full_test 06 Nov 2008, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT) added opt param to get_type_opt and get_type_list had to modify calls in make_random_timing.py and gen_epi_review.py
03 Nov 2008, ZS Saad, 3dNLfim, level 1 (MICRO), type 2 (NEW_OPT) Added Exp (single exponential) model 03 Nov 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Several changes Finished -gltsym, -Rglt, and -Oglt options = add GLTs on the 3dREMLfit command line and output those exclusively to new files. Modified -addbase and -slibase to do censoring if input 1D files are the same length as the uncensored matrix. Also fixed bugs in -ABfile. Oopsie.
31 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added -show_timing_stats option Also, made a small change affecting timing (old results will not match).
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added -offset option 27 Oct 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -regress_motion_file option
23 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Added -rout option, by popular 'demand' 23 Oct 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added lists_are_same function
20 Oct 2008, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT) added write_text_to_file function 20 Oct 2008, RC Reynolds, afni_driver.c, level 2 (MINOR), type 2 (NEW_OPT) added 'GETENV' to the list of DRIVE_AFNI commands
17 Oct 2008, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT) -crop is a new option for cropping an image
03 Oct 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) SUMA accepts text, images, and textures as Displayable Objects See SUMA's interactive help for ctrl+alt+s for more information on Displayable Objects (DOs). The new DOs are in a simple NIML format. It is simplest to look at the script @DO.examples for illustrations of the various forms of DOs that SUMA supports. Sample NIML DOs (called NIDOs) are now provided with the distribution They are called demo.*.niml.do. 03 Oct 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) -viewer_position/_width/_height/_size to control window placement See DriveSuma -help for details.
30 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) added -gltsym option Makes it easy for the user to add GLTs without using 3dDeconvolve.
25 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) added -usetemp option Saves REML setup matrices for various cases to tmp disk files. Is necessary for -slibase and -Grid 5 combined, if anyone ever actually wants to run such a case.
24 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) -addbase and -slibase options to add baseline columns to matrix In particular, -slibase is intended for per-slice modeling of physiological noise effects. Sucks up a lot of memory and CPU time.
23 Sep 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -remove_preproc_files option (akin to -move_preproc_files)
17 Sep 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT) added -labels option, for including labels in filenames
16 Sep 2008, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT) -node_path_do outputs the shortest path between two nodes The shortest path(s) are stored as a SUMA Displayable Object which can be loaded into SUMA with ctrl+alt+s or using DriveSuma. 16 Sep 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT) -load_do sends SUMA Displayable Objects to be rendered See SUMA's interactive help for ctrl+alt+s for more information on Displayable Objects.
02 Sep 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT) -allcostX1D option (for Chairman Z)
25 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Added residual outputs to 3dREMLfit.
22 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT) Add FDR curves and -?fitts options. 22 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) added DRIVE_WAIT command string The command will be executed after the first volume is processed, which is good for opening windows appropriate to a new dataset. 22 Aug 2008, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT) added -drive_wait option
21 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT) added -disable_done option to safeguard real-time mode
03 Aug 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old
31 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT) added HELLO version 2 to work as -disp_all See 'HELLO versions' from 'serial_helper -help' for details. See 'example E' from 'Dimon -help' for a complete testing example. 31 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) enhancements to communication with serial helper - added 'Motion Only' to methods - parameter methods can easily be switched per run - SEND_VER replaces HELLO_VER as Y/N variable 31 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -num_slices option, and full real-time example E
30 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT) added HELLO version 1 and -show_times option 30 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) added HELLO version 1 and show_times option These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES.
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT) added -base1_dset option, where -base1 value can vary over voxels Added for M Beauchamp.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT) added -disp_all to give formatted display of 'all' mask data This was added for P Kundu. 16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT) added choice of 'Vals to Send' to serial_helper Can now send index,i,j,k,x,y,z,value for every value in mask.
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added -sleep_init, -sleep_vol, -sleep_frac These options control the timeout periods between data checks.
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added -gen_epi_review and -no_epi_review options By default, a drive_afni script to review EPI data is now generated.
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added -past_entries option
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT) added nifti_compiled_with_zlib() 13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -with_zlib, and ability to add extensions via 'file:FILENAME' extension update added for J. Gunter
12 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT) added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D also, updated find_last_space to deal with long strings
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT) Add -ARMA option to estimate ARMA(1,1) parameters
21 May 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT) added -amplitudes option (for Rutvik Desai)
20 May 2008, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT) Make TCP/IP to 'localhost' the default. Add option '-shm' if needed.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT) added options for TR-locking and storing '3dDeconvolve -nodata' examples - added shuffle() to replace that from random (cannot produce all perms) - added options -tr, -tr_locked and -save_3dd_cmd - changed -stim_time option to -stim_dur
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT) added -n_rand and -n_randseed
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -set_extern_filelist option, and help for using external data files 13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT) gifticlib-1.0.0: initial release includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT) Added option -1Dformat to output results in 1D format
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT) added get_type_list and other accessor functions
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -copy_gifti_meta and -copy_DA_meta options 28 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 2 (NEW_OPT) added routines to copy MetaData
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT) Added -align_centers as an option to deal with very large moves It used to be that users had to run @Align_Centers on all their data when big moves were needed to align the surface's antaomy to that of the experiment. This is no longer needed. 26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT) Add -norm2 and -normx options: normalize time series before plotting
25 Mar 2008, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT) Added option -ixmat_1D to apply inverse of affine transform
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) added GERT_Reco options (request of D Glen) -gert_filename : specify a name for the GERT_Reco script -gert_nz : override nz=1 in mosaic image files -gert_to3d_prefix : specify a dataset prefix for the to3d command
21 Mar 2008, ZS Saad, 3dnvals, level 1 (MICRO), type 2 (NEW_OPT) Added -all to 3dnvals to output all 4 dimensions.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT) Add -polort option, to keep Gang Chen happy.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT) added -compare_gifti option See 'gifti_tool -help' for details, including example #7. 18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT) added comparison functions to gifticlib
17 Mar 2008, ZS Saad, lpc_align.py, level 1 (MICRO), type 2 (NEW_OPT) Added -big_move and -partial_coverage. -big_move is for when large displacements are needed for alignment. -partial_coverage is for when EPI covers a portion of the brain.
14 Mar 2008, RW Cox, 3dROIstats, level 1 (MICRO), type 2 (NEW_OPT) Sub-brick label printing (and -nobriklab option) Per the noble Vince Hradil.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT) added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT) applied -gert_outdir in the case of dicom images
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) Color map in surface controller can be flipped and rotated * f key for flipping colormap * Up/Down keys for rotating color map * Home for home Hit ctrl+h on Surface Controller's colormap for more help.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT) added '-fitts' option to produce fitted time series dataset
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT) added -accumulate option, to output each partial sum for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 2 (NEW_OPT) Small changes to make onscreen wordwrap match printout wordwrap
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added a TYPE, -type, a new level, and a string to identify each level
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT) allow constraints on sign of deconvolved function 28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT) allow combination of penalty functions in deconvolution 28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT) added -list_authors option and adjusted spacing
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT) add deconvolution via the '-FALTUNG' option Unlike 3dDeconvolve, this deconvolution is to find the input time series, given the impulse response function.
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT) add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT) add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file '-eigonly' causes 3dpc to print eigenvalues to stdout and stop there. '-reduce n pp' outputs a reduced dataset, using only the largest 'n' eigenvalues.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT) add '-1D:' option, to write output that is usable on the command line Sample usage: 1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'` The backquotes `...` capture command's output and put this string on the command line. The '-1D:' option formats the 1deval output so that it is ready to be used in this way.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) An option to show all of suma's environment variables See help for -environment in suma -help.
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest. * Fix little problems with AFNI threshold scale display as q-value alters. * Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks. * Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT) Older History stuff * FDR thresh-vs-z(q) curve generation and storage in datasets. * Display FDR q in AFNI pval label. * Generate FDR curves automatically in 3dDeconvolve, and with '-addFDR' option in 3drefit.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) added options to estimate smoothness in data for use in AlphaSim See help options -regress_est_blur_epits and -regress_est_blur_errts.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c. * mri_fdrize.c function for FDR-z conversion.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT) Older History stuff * Clusterize reporting window.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Add -jpg and -png options to 1dplot.c. * Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c * For ragged 1D input files, arbitrary text starting with alphabetic character is same as '*' for filler. * AFNI_RESCAN_AT_SWITCH is on by default now. * 1dplot takes a 1 row file and flips it to a column for plotting; however , when 2 single row files were input, they'd be catenated and THEN flipped, producing erroneous joined plot. Now, they are flipped THEN catenated, which does the right thing. * Speaking of 1dplot, '-nopush' now works for multiple graphs, rather than just for '-one'. * Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors, and so that '-seed 0' generates a custom seed. * Add some extra text to the 'Clusterize' label (afni_setup.c) to explain that rmm=0 means NN clustering with vmul in voxel count.
12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Changes to bbox.c to add an arrowval index selector to the single-select ion mode strlist chooser (per Shruti Japee's unreasonable demand).
11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Modify edt_filtervol.c to clip off voxels outside the fmask. * Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.
10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option; '-autoweight' now the default for '-ls' cost function. * Re-insert older fixes to afni.c that were lost in CVS.
20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT) Older History stuff * First version of '-lpc' Local Pearson Correlation cost function in 3dAllineate.c, with rhombic dodecahedra as the default building bloks.
14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20. * Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti c.
08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).
31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT) Older History stuff * Make -cmass the default in 3dAllineate.c. * Also add '+clip' feature to '-autoweight' in 3dAllineate.c.
15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT) High resolution image saving with ctrl+r Very high resolution images can be created. See suma's interactive help 'ctrl+h' for more info.
01 Dec 2005, G Chen, 3dANOVA3, level 3 (MAJOR), type 2 (NEW_OPT) New options to run 2nd-order general linear contrasts in 3dANOVA3. See more details on: https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
15 Jan 2003, RC Reynolds, Imon, level 3 (MAJOR), type 2 (NEW_OPT) added connection to the realtime plugin in afni

auto-generated by afni_history on Oct 17 2019