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cat_defaults.m
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function cat_defaults
% Sets the defaults for CAT
% FORMAT cat_defaults
%_______________________________________________________________________
%
% This file is intended to be customised for the site.
%
% Care must be taken when modifying this file
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$
clear global cat;
global cat
% CAT12 installation folder
catdir = fileparts(which('cat12'));
% Options for inital SPM12 segmentation that is used as starting point for CAT12.
%=======================================================================
cat.opts.tpm = {fullfile(spm('dir'),'tpm','TPM.nii')};
cat.opts.ngaus = [1 1 2 3 4 2]; % Gaussians per class (SPM12 default = [1 1 2 3 4 2]) - alternative: [3 3 2 3 4 2]
cat.opts.affreg = 'mni'; % Affine regularisation (SPM12 default = mni) - '';'mni';'eastern';'subj';'none';'rigid'
cat.opts.warpreg = [0 0.001 0.5 0.05 0.2]; % Warping regularisation (SPM12 default) - no useful modification found
cat.opts.tol = 1e-4; % SPM preprocessing accuracy (CAT only!) - 1e-2 very low accuracy (fast); 1e-4 default; 1e-6 very high accuracy (slow)
cat.opts.accstr = 0.5; % SPM preprocessing accuracy (CAT only!) - 0 very low accuracy (fast) .. 1 very high accuracy (slow); default = 0.5
cat.opts.biasstr = 0.5; % Strength of the bias correction that controls the biasreg and biasfwhm parameter (CAT only!)
% 0 - use SPM parameter; eps - ultralight, 0.25 - light, 0.5 - medium, 0.75 - strong, and 1 - heavy corrections
% job.opts.biasreg = min( 10 , max( 0 , 10^-(job.opts.biasstr*2 + 2) ));
% job.opts.biasfwhm = min( inf , max( 30 , 30 + 60*job.opts.biasstr ));
cat.opts.biasreg = 0.001; % Bias regularisation (cat.opts.biasstr has to be 0!) - 10,1,0.1,...,0.00001
% smaller values for stronger bias fields
cat.opts.biasfwhm = 60; % Bias FWHM (cat.opts.biasstr has to be 0!) - 30:10:120,inf
% lower values for strong bias fields, but check for overfitting of the thalamus (values <45 mm)
cat.opts.samp = 3; % Sampling distance - alternative: 1.5
% Initial SPM segmentation resolution, whereas the AMAP runs on the full or specified resolution
% described by cat.extopts.restype and cat.extopts.resval. Higher resolution did not improve the
% results in most results (but increase calculation time were.
cat.opts.redspmres = 0.0; % limit image resolution for internal SPM preprocessing output in mm (default: 1.0)
% Writing options
%=======================================================================
% options:
% native 0/1 (none/yes)
% warped 0/1 (none/yes)
% mod 0/1/2/3 (none/affine+nonlinear/nonlinear only/both)
% dartel 0/1/2/3 (none/rigid/affine/both)
% save surface and thickness
cat.output.surface = 1; % surface and thickness creation: 0 - no (default), 1 - lh+rh, 2 - lh+rh+cerebellum,
% 3 - lh, 4 - rh, 5 - lh+rh (fast, no registration, only for quick quality check and not for analysis),
% 6 - lh+rh+cerebellum (fast, no registration, only for quick quality check and not for analysis)
% 9 - thickness only (for ROI analysis, experimental!)
% +10 to estimate WM and CSF width/depth/thickness (experimental!)
% save ROI values
cat.output.ROI = 1; % write xml-file with ROI data (0 - no, 1 - yes (default))
% bias and noise corrected, global intensity normalized
cat.output.bias.native = 0;
cat.output.bias.warped = 1;
cat.output.bias.dartel = 0;
% bias and noise corrected, (locally - if LAS>0) intensity normalized
cat.output.las.native = 0;
cat.output.las.warped = 0;
cat.output.las.dartel = 0;
% GM tissue maps
cat.output.GM.native = 0;
cat.output.GM.warped = 0;
cat.output.GM.mod = 1;
cat.output.GM.dartel = 0;
% WM tissue maps
cat.output.WM.native = 0;
cat.output.WM.warped = 0;
cat.output.WM.mod = 1;
cat.output.WM.dartel = 0;
% CSF tissue maps
cat.output.CSF.native = 0;
cat.output.CSF.warped = 0;
cat.output.CSF.mod = 0;
cat.output.CSF.dartel = 0;
% WMH tissue maps (only for opt.extopts.WMHC==3) - in development
cat.output.WMH.native = 0;
cat.output.WMH.warped = 0;
cat.output.WMH.mod = 0;
cat.output.WMH.dartel = 0;
% stroke lesion tissue maps (only for opt.extopts.SLC>0) - in development
cat.output.SL.native = 0;
cat.output.SL.warped = 0;
cat.output.SL.mod = 0;
cat.output.SL.dartel = 0;
% label
% background=0, CSF=1, GM=2, WM=3, WMH=4 (if opt.extopts.WMHC==3), SL=1.5 (if opt.extopts.SLC>0)
cat.output.label.native = 1;
cat.output.label.warped = 0;
cat.output.label.dartel = 0;
% Tissue classes 4-6 to create own TPMs
cat.output.TPMC.native = 0;
cat.output.TPMC.warped = 0;
cat.output.TPMC.mod = 0;
cat.output.TPMC.dartel = 0;
% cortical thickness (experimental)
cat.output.ct.native = 0;
cat.output.ct.warped = 0;
cat.output.ct.dartel = 0;
% percentage position (experimental)
cat.output.pp.native = 0;
cat.output.pp.warped = 0;
cat.output.pp.dartel = 0;
% jacobian determinant 0/1 (none/yes)
cat.output.jacobian.warped = 0;
% deformations
% order is [forward inverse]
cat.output.warps = [1 0];
% transformations
% order is affine rigid (both forward and inverse)
cat.output.rmat = 0;
% Expert options
%=======================================================================
% general GUI compatible definition of most *str parameter:
% 0 - no correction
% eps - ultralight correction
% 0.25 - light correction
% 0.50 - medium correction
% 0.75 - strong correction
% 1 - heavy correction
% [inf - automatic correction]
% skull-stripping options
cat.extopts.gcutstr = 2; % Strength of skull-stripping: 0 - SPM approach; eps to 1 - gcut; 2 - new APRG approach; -1 - no skull-stripping (already skull-stripped); default = 2
cat.extopts.cleanupstr = 0.5; % Strength of the cleanup process: 0 to 1; default 0.5
% segmentation options
cat.extopts.spm_kamap = 0; % Replace initial SPM by k-means AMAP segm. 0 - Unified Segmentation, 2 - k-means AMAP
cat.extopts.NCstr =-Inf; % Strength of the noise correction: 0 to 1; 0 - no filter, -Inf - auto, 1 - full, 2 - ISARNLM (else SANLM), default -Inf
cat.extopts.LASstr = 0.5; % Strength of the local adaptation: 0 to 1; default 0.5
cat.extopts.BVCstr = 0.5; % Strength of the Blood Vessel Correction: 0 to 1; default 0.5
cat.extopts.regstr = 0.5; % Strength of Shooting registration: 0 - Dartel, eps (fast), 0.5 (default) to 1 (accurate) optimized Shooting, 4 - default SPM Shooting
cat.extopts.WMHC = 2; % Correction of WM hyperintensities: 0 - no correction, 1 - only for Dartel/Shooting
% 2 - also correct segmentation (to WM), 3 - handle as separate class; default 1
cat.extopts.WMHCstr = 0.5; % Strength of WM hyperintensity correction: 0 to 1; default 0.5
cat.extopts.SLC = 0; % Stroke lesion correction (SLC): 0 - no correction, 1 - handling of manual lesion that have to be set to zero!
% 2 - automatic lesion detection (in development)
cat.extopts.mrf = 1; % MRF weighting: 0 to 1; <1 - weighting, 1 - auto; default 1
% resolution option
cat.extopts.restype = 'optimal'; % resolution handling: 'native','fixed','best', 'optimal'
cat.extopts.resval = [1.0 0.30]; % resolution value and its tolerance range for the 'fixed' and 'best' restype
% use BIDS data structure
[cat_ver, cat_rel] = cat_version;
cat.extopts.bids_folder = fullfile('..','derivatives',[cat_ver '_' cat_rel]); % default relative BIDS path for saving data
cat.extopts.bids_yes = 0; % use BIDS structure for saving data
% check for multiple cores is different for octave
if strcmpi(spm_check_version,'octave')
cat.extopts.nproc = nproc;
else
cat.extopts.nproc = feature('numcores');
end
%{
native:
Preprocessing with native resolution.
In order to avoid interpolation artifacts in the Dartel output the lowest spatial resolution is always limited to the voxel size of the normalized images (default 1.5mm).
Examples:
native resolution internal resolution
0.95 0.95 1.05 > 0.95 0.95 1.05
0.45 0.45 1.70 > 0.45 0.45 1.70
best:
Preprocessing with the best (minimal) voxel dimension of the native image or at least 1.0 mm.'
The first parameters defines the lowest spatial resolution for every dimension, while the second is used to avoid tiny interpolations for almost correct resolutions.
In order to avoid interpolation artifacts in the Dartel output the lowest spatial resolution is always limited to the voxel size of the normalized images (default 1.5mm).
Examples:
Parameters native resolution internal resolution
[1.00 0.10] 0.95 1.05 1.25 > 0.95 1.05 1.00
[1.00 0.10] 0.45 0.45 1.50 > 0.45 0.45 1.00
[0.75 0.10] 0.45 0.45 1.50 > 0.45 0.45 0.75
[0.75 0.10] 0.45 0.45 0.80 > 0.45 0.45 0.80
[0.50 0.10] 0.45 0.45 0.80 > 0.45 0.45 0.50
[0.50 0.30] 0.50 0.50 1.50 > 0.50 0.50 0.50
[0.50 0.30] 1.50 1.50 3.00 > 1.50 1.50 1.50
[0.00 0.10] 0.45 0.45 1.50 > 0.45 0.45 0.45
fixed:
This options prefers an isotropic voxel size that is controlled by the first parameter.
The second parameter is used to avoid tiny interpolations for almost correct resolutions.
In order to avoid interpolation artifacts in the Dartel output the lowest spatial resolution is always limited to the voxel size of the normalized images (default 1.5mm).
There is no upper limit, but we recommend to avoid unnecessary interpolation.
Examples:
Parameters native resolution internal resolution
[1.00 0.10] 0.45 0.45 1.70 > 1.00 1.00 1.00
[1.00 0.10] 0.95 1.05 1.25 > 0.95 1.05 1.00
[1.00 0.02] 0.95 1.05 1.25 > 1.00 1.00 1.00
[0.75 0.10] 0.75 0.95 1.25 > 0.75 0.75 0.75
optimal:
This option prefers an isotropic voxel size that is controlled by the median voxel size and a volume term that deals with highly anisotropic voxels.
The first parameter controls the lower resolution limit, while the second parameter is used to avoid tiny interpolations for almost correct resolutions.
Examples:
Parameters native resolution internal resolution
[1.00 0.10] 0.50 0.50 0.90 > 0.50 0.50 0.60
[1.00 0.10] 0.50 0.50 1.00 > 0.70 0.70 0.70
[1.00 0.30] 0.50 0.50 1.00 > 0.50 0.50 0.70
[1.00 0.10] 0.80 0.80 1.00 > 0.80 0.80 1.00
[1.00 0.10] 0.45 0.45 1.70 > 0.90 0.90 0.90
[1.00 0.10] 0.95 1.05 1.25 > 0.95 1.05 1.00
[1.00 0.30] 0.95 1.05 1.25 > 0.95 1.05 1.25
%}
% registration and normalization options
% Subject species: - 'human';'ape_greater';'ape_lesser';'monkey_oldworld';'monkey_newwold' (in development)
cat.extopts.species = 'human';
% Affine PreProcessing (APP) with rough bias correction and brain extraction for special anatomies (nonhuman/neonates)
cat.extopts.APP = 1070; % 0 - none; 1070 - default; [1 - light; 2 - full; 1144 - update of 1070, 5 - animal (no affreg)]
cat.extopts.setCOM = 1; % 0 - none; 1 - use center-of-mass to estimate origin as starting value for affine registration
cat.extopts.vox = 1.5; % voxel size for normalized data (EXPERIMENTAL: inf - use Tempate values)
cat.extopts.bb = 12; % boundary box: 12 - [-84 -120 -72;84 84 96]; 16 - [-90 -126 -72;90 90 108]
cat.extopts.shootingsurf = 'Template_T1'; % Shooting surface name
cat.extopts.pth_templates = fullfile(catdir,'templates_MNI152NLin2009cAsym'); % Templates and atlases folder for volumes
cat.extopts.darteltpm = {fullfile(cat.extopts.pth_templates,'Template_1_Dartel.nii')}; % Indicate first Dartel template (Template_1)
cat.extopts.shootingtpm = {fullfile(cat.extopts.pth_templates,'Template_0_GS.nii')}; % Indicate first Shooting template (Template 0) - not working
cat.extopts.shootingT1 = {fullfile(cat.extopts.pth_templates,'Template_T1_masked.nii')}; % T1 for result overlay, choose Template_T1.nii for non-masked T1
cat.extopts.brainmask = {fullfile(cat.extopts.pth_templates,'brainmask.nii')}; % Brainmask for affine registration
cat.extopts.T1 = {fullfile(cat.extopts.pth_templates,'T1.nii')}; % T1 for affine registration
cat.extopts.cat12atlas = {fullfile(cat.extopts.pth_templates,'cat.nii')}; % CAT atlas with major regions for VBM, SBM & ROIs
% surface options
cat.extopts.pbtres = 0.5; % internal resolution for thickness estimation in mm (default 0.5)
cat.extopts.SRP = 30; % surface recontruction pipeline & self-intersection correction:
% 0/1 - CS1 without/with/with-optimized SIC
% 20/21/22 - CS2 without/with/with-optimized SIC
% 30 - CS3
cat.extopts.reduce_mesh = 1; % optimize surface sampling: 0 - PBT res. (slow); 1 - optimal res. (default); 2 - internal res.; 3 - SPM init; 4 - MATLAB init; 5 - SPM full;
% 6 - MATLAB full; 7 - MATLAB full ext.;
cat.extopts.vdist = 2; % mesh resolution (experimental, do not change!)
cat.extopts.pbtlas = 0; % reduce myelination effects (experimental, not yet working properly!)
cat.extopts.thick_measure = 1; % distance method for estimating thickness: 1 - Tfs: Freesurfer method using mean(Tnear1,Tnear2) (default in 12.7+); 0 - Tlink: linked distance (used before 12.7)
cat.extopts.thick_limit = 5; % upper limit for Tfs thickness measure similar to Freesurfer (only valid if cat.extopts.thick_measure is set to "1"
cat.extopts.close_parahipp = 1; % optionally apply closing inside mask for parahippocampal gyrus to get rid of deep holes that lead to large
% cuts in gyri after topology correction. However, this may also lead to poorer quality of topology
% correction for other data and should be only used if large cuts in the parahippocampal areas occur
cat.extopts.scale_cortex = 0.7; % scale intensity values for cortex to start with initial surface that is closer to GM/WM border to prevent that gyri/sulci are glued
% if you still have glued gyri/sulci (mainly in the occ. lobe) you can try to decrease this value (start with 0.6)
% please note that decreasing this parameter also increases the risk of an interrupted parahippocampal gyrus
cat.extopts.add_parahipp = 0.1; % increase values in the parahippocampal area to prevent large cuts in the parahippocampal gyrus (initial surface in this area
% will be closer to GM/CSF border)
% if the parahippocampal gyrus is still cut you can try to increase this value (start with 0.15)
% visualisation, print, developing, and debugging options
cat.extopts.colormap = 'BCGWHw'; % {'BCGWHw','BCGWHn'} and matlab colormaps {'jet','gray','bone',...};
cat.extopts.report.color = []; % report color setting invert fontcolor if dark: [] - use figure color; 0.95 - light gray; [0.1 0.15 0.2] - dark blue
cat.extopts.verb = 2; % verbose output: 1 - default; 2 - details; 3 - write debugging files
cat.extopts.ignoreErrors = 1; % catch errors: 0 - stop with error (default); 1 - catch preprocessing errors and proceed with next subject (requires MATLAB 2008 or higher);
% 2 - catch preprocessing errors and try backup function if this also fails then proceed with the next subject (requires MATLAB 2008 or higher)
cat.extopts.expertgui = 0; % control of user GUI: 0 - common user modus with simple GUI; 1 - expert modus with extended GUI; 2 - developer modus with full GUI
cat.extopts.subfolders = 1; % use subfolders such as mri, surf, report, and label to organize your data (this option is ignored if BIDS structure is found in your data)
cat.extopts.experimental = 0; % experimental functions: 0 - default, 1 - call experimental unsafe functions
cat.extopts.print = 2; % display and print out pdf-file of results: 0 - off, 1 - volume only (use this to avoid problems on servers that do not support openGL),
% 2 - volume and surface (default)
cat.extopts.fontsize = get(0,'defaultuicontrolFontSize'); % default font size for GUI;
%cat.extopts.fontsize = spm('FontSizes',7); % set default font size for GUI manually; increase value for larger fonts or set it to
cat.extopts.send_info = 1; % send Matlab and CAT12 version to SBM server for internal statistics only. If you don't want to send this
% information set this flag to "0". See online help CAT12->CAT12 user statistics for more information
cat.extopts.gifti_dat = 1; % save gifti files after resampling with external dat-file, which increases speed of gifti-processing and keeps SPM.mat file small
% because the cdata field is not saved with full data in SPM.mat.
% always use expert mode for standalone installations
if isdeployed, cat.extopts.expertgui = 1; end
% Expert options - ROIs
%=======================================================================
% ROI maps from different sources mapped to Dartel CAT-space of IXI-template
% { filename , GUIlevel , tissue , use }
% filename = '' - path to the ROI-file
% GUIlevel = [ 0 | 1 | 2 ] - avaible in GUI level
% tissue = {['csf','gm','wm','brain','none']} - tissue classes for volume estimation
% use = [ 0 | 1 ] - default setting to use this atlas
cat.extopts.atlas = { ...
fullfile(cat.extopts.pth_templates,'neuromorphometrics.nii') 0 {'csf','gm','wm'} 1; ... % atlas based on 35 subjects
fullfile(cat.extopts.pth_templates,'lpba40.nii') 0 {'gm','wm'} 1; ... % atlas based on 40 subjects
fullfile(cat.extopts.pth_templates,'cobra.nii') 0 {'gm','wm'} 1; ... % hippocampus-amygdala-cerebellum-subcortex, 5 subjects, 0.6 mm voxel size
fullfile(cat.extopts.pth_templates,'hammers.nii') 0 {'csf','gm','wm'} 0; ... % atlas based on 30 subjects with 95 regions
fullfile(cat.extopts.pth_templates,'thalamus.nii') 0 {'gm'} 1; ... % thalamic nuclei based on DTI from 70 subjects with 14 regions
fullfile(cat.extopts.pth_templates,'thalamic_nuclei.nii') 0 {'gm'} 1; ... % thalamic nuclei based on hi-res T2 from 9 subjects with 22 regions
fullfile(cat.extopts.pth_templates,'suit.nii') 0 {'gm','wm'} 1; ... % cerebellar lobes from 20 subjects
fullfile(cat.extopts.pth_templates,'ibsr.nii') 0 {'csf','gm','wm'} 0; ... % less regions, 18 subjects, low-res T1 image quality
fullfile(cat.extopts.pth_templates,'aal3.nii') 1 {'gm'} 0; ... % many regions, but only labeled on one subject
fullfile(cat.extopts.pth_templates,'mori.nii') 1 {'gm','wm'} 0; ... % only one subject, but with WM regions
fullfile(cat.extopts.pth_templates,'anatomy3.nii') 1 {'gm','wm'} 0; ... % 93 regions, 10 subjects
fullfile(cat.extopts.pth_templates,'julichbrain.nii') 1 {'gm','wm'} 0; ... % many regions, 10 subjects
fullfile(cat.extopts.pth_templates,'Tian_Subcortex_S4_7T.nii') 1 {'gm'} 0; ... % 62 subcortical regions, 183 subjects
fullfile(cat.extopts.pth_templates,'Schaefer2018_100Parcels_17Networks_order.nii') 1 {'gm','wm'} 0; ... % atlas based on rsfMRI data from 1489 subjects
fullfile(cat.extopts.pth_templates,'Schaefer2018_200Parcels_17Networks_order.nii') 1 {'gm','wm'} 0; ... % atlas based on rsfMRI data from 1489 subjects
fullfile(cat.extopts.pth_templates,'Schaefer2018_400Parcels_17Networks_order.nii') 1 {'gm','wm'} 0; ... % atlas based on rsfMRI data from 1489 subjects
fullfile(cat.extopts.pth_templates,'Schaefer2018_600Parcels_17Networks_order.nii') 1 {'gm','wm'} 0; ... % atlas based on rsfMRI data from 1489 subjects
};
% { name fileid GUIlevel use } - in development
cat.extopts.satlas = { ...
'Desikan' fullfile(catdir,'atlases_surfaces','lh.aparc_a2009s.freesurfer.annot') 0 1;
'Destrieux' fullfile(catdir,'atlases_surfaces','lh.aparc_DK40.freesurfer.annot') 0 1;
'HCP' fullfile(catdir,'atlases_surfaces','lh.aparc_HCP_MMP1.freesurfer.annot') 0 0;
... Schaefer atlases ...
'Schaefer2018_100P_17N' fullfile(catdir,'atlases_surfaces','lh.Schaefer2018_100Parcels_17Networks_order.annot') 1 0;
'Schaefer2018_200P_17N' fullfile(catdir,'atlases_surfaces','lh.Schaefer2018_200Parcels_17Networks_order.annot') 0 0;
'Schaefer2018_400P_17N' fullfile(catdir,'atlases_surfaces','lh.Schaefer2018_400Parcels_17Networks_order.annot') 1 0;
'Schaefer2018_600P_17N' fullfile(catdir,'atlases_surfaces','lh.Schaefer2018_600Parcels_17Networks_order.annot') 1 0;
};
%=======================================================================
% PRIVATE PARAMETERS (NOT FOR GENERAL USE)
%=======================================================================
% Additional maps
%=======================================================================
% atlas maps (for evaluation)
cat.output.atlas.native = 0;
cat.output.atlas.warped = 0;
cat.output.atlas.dartel = 0;
% IDs of the ROIs in the cat atlas map (cat.nii). Do not change this!
cat.extopts.LAB.NB = 0; % no brain
cat.extopts.LAB.CT = 1; % cortex
cat.extopts.LAB.CB = 3; % Cerebellum
cat.extopts.LAB.BG = 5; % BasalGanglia
cat.extopts.LAB.BV = 7; % Blood Vessels
cat.extopts.LAB.TH = 9; % Hypothalamus
cat.extopts.LAB.ON = 11; % Optical Nerve
cat.extopts.LAB.MB = 13; % MidBrain
cat.extopts.LAB.BS = 13; % BrainStem
cat.extopts.LAB.VT = 15; % Ventricle
cat.extopts.LAB.NV = 17; % no Ventricle
cat.extopts.LAB.HC = 19; % Hippocampus
cat.extopts.LAB.HD = 21; % Head
cat.extopts.LAB.HI = 23; % WM hyperintensities
cat.extopts.LAB.PH = 25; % Gyrus parahippocampalis
cat.extopts.LAB.LE = 27; % lesions