Dear Jurjen,
forgot to mention, that you can use the following options to skip Dartel registration. However, this will only save time and the skull-stripping will be unaffected:
- deselect ROI analysis (No ROI processing)
- deselect Grey Matter / Modulated normalized
- deselect White Matter / Modulated normalized
- deselect Bias, noise and global intensity corrected T1 image / Normalized
Best,
Christian
On Thu, 9 May 2019 09:25:48 +0100, Jurjen Heij <[log in to unmask]> wrote:
>Dear CAT12/SPM experts,
>
>I'm currently working with high-resolution structural data from our 7T system. The usual brain extraction programs don't work satisfactorily, so I intended on trying the CAT12 toolbox. The initial results seem pretty good, but I'm wondering to what extend it registers to other templates (e.g., the Dartel registration)?
>
>I just want to use it for its skull-stripping capabilities, and use ANTs for other registration purposes. Any idea how to turn off registration related options and just have the skull-stripping option? I attached my script on the bottom with the current settings.
>
>Thank you in advance.
>
>Best,
>
>Jurjen Heij
>Berlin Ultrahigh Field Facility (BUFF)
>Max Delbruck Center for Molecular Medicine
>
>Script:
>addpath(genpath('/home/fsluser/spm12'));
>addpath(genpath('/mnt/hgfs/Shared/bold'));
>
>spm_jobman('initcfg');
>
>pathDir = '/mnt/hgfs/Shared/bold/test';
>subfolder = dir(fullfile(pathDir, '*'));
>subfolder = setdiff({subfolder([subfolder.isdir]).name},{'.','..'});
>
>for ii = 1:numel(subfolder)
> newPath = fullfile(pathDir, subfolder{1, ii});
> cd(newPath);
>
> matlabbatch{1}.spm.tools.cat.estwrite.data = {'structural.nii'};
> matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {'/home/fsluser/spm12/tpm/TPM.nii'};
> matlabbatch{1}.spm.tools.cat.estwrite.opts.affreg = 'none';
> matlabbatch{1}.spm.tools.cat.estwrite.opts.biasstr = 0.5;
> matlabbatch{1}.spm.tools.cat.estwrite.opts.accstr = 0.5;
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.APP = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.LASstr = 0.5;
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.gcutstr = 2;
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.registration.dartel.darteltpm = {'/home/fsluser/spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii'};
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.vox = 0.75;
> matlabbatch{1}.spm.tools.cat.estwrite.extopts.restypes.best = [0.5 0.1];
> matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native = 1;
> matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native = 1;
> matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.labelnative = 1;
> matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.jacobianwarped = 0;
> matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [0 0];
>
> spm('defaults','FMRI')
> spm_jobman('run', matlabbatch);
>
>end
>exit
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