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iCAPs/packages/spm12/config/spm_cfg_tissue_volumes.m
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spm_cfg_tissue_volumes.m
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function tvol = spm_cfg_tissue_volumes
% SPM Configuration file for Tissue Volumes
%
% See also: spm_run_tissue_volumes, spm_summarise
%__________________________________________________________________________
% Copyright (C) 2013-2016 Wellcome Trust Centre for Neuroimaging
% Ged Ridgway
% $Id: spm_cfg_tissue_volumes.m 6952 2016-11-25 16:03:13Z guillaume $
mat = cfg_files;
mat.tag = 'matfiles';
mat.name = 'Segmentation mat-files';
mat.filter = 'mat';
mat.ufilter = 'seg8\.mat$';
mat.num = [1 Inf];
mat.help = {
'Select the ''seg8.mat'' files containing the segmentation parameters.'
};
T = cfg_entry;
T.tag = 'tmax';
T.name = 'Maximum tissue class';
T.strtype = 'n';
T.num = [1 1];
T.val = {3};
T.help = {
['Specify the maximum tissue class, T, where tissues 1:T will be ' ...
'measured.']
['The default of 3 corresponds to GM, WM and CSF for the ' ...
'default tissue prior probability maps ''TPM.nii,1'' to ''TPM.nii,3''']
''
['The sum of these tissues will also be computed, which by ' ...
'default is the total intracranial volume (known as TIV or ICV). ' ...
'If T=2, the sum will by default be the total parenchymal brain ' ...
'volume (known as TBV or PBV), which is also often of interest.']
};
mask = cfg_files;
mask.tag = 'mask';
mask.name = 'Mask image';
mask.filter = 'image';
mask.num = [0 1];
mask.val = {{fullfile(spm('dir'), 'tpm', 'mask_ICV.nii,1')}};
mask.help = {
'Optional binary mask image in same space as TPMs (e.g. MNI).'
'Only voxels inside this mask will count for the total volume.'
''
['The default mask excludes the eyes, which might otherwise be ' ...
'counted in the fluid tissue class (that includes cerebrospinal, ' ...
'aqueous, and vitreous fluids/humours).']
};
outf = cfg_entry;
outf.tag = 'outf';
outf.name = 'Output file';
outf.strtype = 's';
outf.val = {''};
outf.help = {
'Filename for saving results.'
['Segmentation filenames and volumes ' ...
'will be stored in CSV format (comma-separated variables).']
''
'This can be empty; results will appear in the MATLAB command window.'
};
tvol = cfg_exbranch;
tvol.tag = 'tvol';
tvol.name = 'Tissue Volumes';
tvol.val = {mat T mask outf};
tvol.help = {
'Compute total tissue volumes (in litres) from segmentation results.'
''
['Only the seg8.mat files are required, but if modulated warped ' ...
'segmentations (mwc*) are found they will be reused, saving time ' ...
'(and allowing you to use non-default values for MRF and/or ' ...
'clean-up options if you wish).']
};
tvol.prog = @(job) spm_run_tissue_volumes('exec', job);
tvol.vout = @(job) spm_run_tissue_volumes('vout', job);
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