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Contents.m
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% Computational Anatomy Toolbox
% Version 2583 (CAT12.9) 2024-05-25
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$
% ==========================================================================
% Description
% ==========================================================================
% This toolbox is a collection of extensions to the segmentation algorithm
% of SPM12 (Wellcome Department of Cognitive Neurology) to provide computational
% morphometry. It is developed by Christian Gaser and Robert Dahnke (Jena
% University Hospital, Departments of Psychiatry and Neurology) and is available
% to the scientific community under the terms of the GNU General Public Licence as
% published by the Free Software Foundation; either version 2 of the Licence,
% or (at your option) any later version.
%
% If you use any CAT12 code for commercial application, please email
% christian.gaser@uni-jena.de.
%
% General files
% INSTALL.txt - installation instructions
% CHANGES.txt - changes in revisions
% Contents.m - this file
%
% Core functions
% cat12.m
% cat_amap.m - compilation wrapper for cat_amap.c
% cat_main.m
% cat_run.m - runtime funtion for CAT12
% cat_run_job.m
% cat_run_newcatch.m
% cat_run_oldcatch.m
% cat_defaults.m - sets the defaults for CAT12
% cat_get_defaults.m - defaults for CAT12
% spm_cat12.m - toolbox wrapper to call CAT12
%
% Utilities
% cat_sanlm.m - Spatial Adaptive Non Local Means Denoising Filter
% cat_update.m - check for new updates
% cat_debug.m - print debug information for SPM12 and CAT12
% cat_ornlm.m
% cat_plot_boxplot.m
% slice_overlay.m - overlay tool
% sliderPanel.m
%
% Input & Output
% cat_io_3Dto4D.m
% cat_io_FreeSurfer.m
% cat_io_cgw2seg.m
% cat_io_checkinopt.m
% cat_io_cmd.m
% cat_io_colormaps.m
% cat_io_cprintf.m
% cat_io_csv.m
% cat_io_handle_pre.m
% cat_io_img2nii.m
% cat_io_matlabversion.m
% cat_io_remat.m
% cat_io_seg2cgw.m
% cat_io_struct2table.m
% cat_io_updateStruct.m
% cat_io_writenii.m
% cat_io_xml.m
% cat_io_xml2csv.m
%
% Longitudinal batch
% cat_long_main.m - longitudinal batch mode
% cat_long_multi_run.m - call cat_long_main for multiple subjects
%
% Statistics
% cat_stat_calc_stc.m
% cat_stat_homogeneity.m - check sample homogeneity across sample
% cat_stat_marks.m
% cat_stat_nanmean.m
% cat_stat_nanmedian.m
% cat_stat_nanstat1d.m
% cat_stat_nanstd.m
% cat_stat_nansum.m
% cat_stat_showslice_all.m - show 1 slice of all images
% cat_stat_spm.m
% cat_stat_spmF2x.m - transformation of F-maps to P, -log(P), R2 maps
% cat_stat_spmT2x.m - transformation of t-maps to P, -log(P), r or d-maps
% cat_stat_TIV.m - read total intracranial volume (TIV) from xml-files
%
% Surface functions
% cat_surf_avg.m
% cat_surf_calc.m
% cat_surf_createCS.m
% cat_surf_display.m
% cat_surf_info.m
% cat_surf_parameters.m
% cat_surf_rename.m
% cat_surf_render.m
% cat_surf_resamp.m
% cat_surf_resamp_freesurfer.m
% cat_surf_resample.m
% cat_surf_smooth.m
% cat_surf_vol2surf.m
%
% Test and experimental functions
% cat_tst_BWPsliceartifact.m
% cat_tst_CJV.m
% cat_tst_calc_kappa.m
% cat_tst_qa.m
% cat_tst_staple_multilabels.m
%
% Volume functions
% cat_vol_approx.m
% cat_vol_atlas.m
% cat_vol_average.m
% cat_vol_calc_roi.m
% cat_vol_correct_slice_scaling.m
% cat_vol_ctype.m
% cat_vol_defs.m - apply deformations to images
% cat_vol_findfiles.m
% cat_vol_groupwise_ls.m
% cat_vol_imcalc.m
% cat_vol_iscale.m
% cat_vol_morph.m - morphological operations to 3D data
% cat_vol_nanmean3.m
% cat_vol_partvol.m
% cat_vol_pbt.m
% cat_vol_resize.m
% cat_vol_sanlm.m - GUI for cat_sanlm
% cat_vol_series_align.m
% cat_vol_set_com.m
% cat_vol_slice_overlay.m - wrapper for overlay tool slice_overlay
% cat_vol_slice_overlay_ui.m - example for user interface for overlay wrapper cat_slice_overlay.m
% cat_vol_smooth3X.m
%
% Batch mode
% cat_batch_long.m - batch mode wrapper for spm_jobman for longitudinal pipeline
% cat_batch_spm.m - batch mode wrapper for spm_jobman for SPM12
% cat_batch_vbm.m - batch mode wrapper for spm_jobman for CAT12
%
% Check input and files
% cat_check.m
% cat_check_system_output.m
%
% Configuration
% cat_conf_extopts.m
% cat_conf_long.m
% cat_conf_opts.m
% cat_conf_stools.m
% cat_conf_stoolsexp.m
% cat_conf_tools.m - wrapper for calling CAT12 utilities
% tbx_cfg_cat.m
%
% Templates/Atlases volumes
% Template_?_GS.nii - Geodesic Shooting template of 555 subjects from IXI database
% in MNI152NLin2009cAsym space provided for 6 different iteration steps
% Template_T1.nii - average of 555 T1 images of IXI database in MNI152 space after
% Geodesic Shooting
% aal3.* - AAL3 atlas
% anatomy2.* - Anatomy2 atlas
% cobra.* - CoBra atlas
% hammers.* - Hammers atlas
% ibsr.* - IBSR atlas
% julichbrain.* _ JulichBrain atlas
% mori.* - Mori atlas
% thalamus.* - Thalamic Nuclei atlas
% neuromorphometrics.* - Neuromorphometrics atlas
% lpba40.nii - LPBA40 atlas
% brainmask.nii - brainmask
% cat12.nii - partitions for hemispheres, subcortical structures and vessels
%
% Templates/Atlases surfaces
% ?h.central.Template_T1.gii
% - central surface of Dartel average brain for result mapping
% ?h.central.freesurfer.gii - central surface of freesurfer fsaverage
% ?h.inflated.freesurfer.gii - inflated surface of freesurfer fsaverage
% ?h.sphere.freesurfer.gii - spherical surface of freesurfer fsvaverage