I'm not quite sure what that batch would do, as it is a mixture of the old
and new segmentations. eg
matlabbatch{3}.spm.spatial.preproc.opts.msk = {''};
matlabbatch{3}.spm.tools.preproc8.warp.reg = 4;
I'd suggest that you try the default segmentation of SPM12b, which attempts
to combine the best of the old and new segmentations of SPM8.
Best regards,
-John
On 30 October 2013 14:26, Rodrigo Perea <[log in to unmask]> wrote:
> Dearl all,
> I am creating a matlabbatch with a Dartel process but with some
> modifications on the segmentations. Apparently my new segmentations will
> get rid of previous dura problems I had before. Anyways, I usually used the
> registered rc1* gray matter for my next step. Thought, I could only get the
> gray matter output c1* without the r* prefix. How can I add a module to
> registered to template using matlabbatch or the GUI module?
> I guess if somebody could expand better or point me to where I can find
> this information about the differences between the prefixes, it will be
> great.
> Thanks in advance,
> Rodrigo
>
>
>
> This step will generate m* mwc*:
>
> matlabbatch{3}.spm.spatial.preproc.data = {ref};
> matlabbatch{3}.spm.spatial.preproc.output.GM = [1 0 1]; %I am
> assuming this is the information needed)
> matlabbatch{3}.spm.spatial.preproc.output.WM = [1 0 1];
> matlabbatch{3}.spm.spatial.preproc.output.CSF = [0 0 0];
> matlabbatch{3}.spm.spatial.preproc.output.biascor = 1;
> matlabbatch{3}.spm.tools.preproc8.channel.write = [0 0];
> matlabbatch{3}.spm.spatial.preproc.output.cleanup = 2;
> matlabbatch{3}.spm.spatial.preproc.opts.tpm = {
> '/usr/local/spm8/tpm/grey.nii'
> '/usr/local/spm8/tpm/white.nii'
> '/usr/local/spm8/tpm/csf.nii'
> };
> matlabbatch{3}.spm.spatial.preproc.opts.ngaus = [2
> 2
> 2
> 4];
> matlabbatch{3}.spm.spatial.preproc.opts.regtype = 'mni';
> matlabbatch{3}.spm.spatial.preproc.opts.warpreg = 1;
> matlabbatch{3}.spm.spatial.preproc.opts.warpco = 25;
> matlabbatch{3}.spm.spatial.preproc.opts.biasreg = 0.0001;
> matlabbatch{3}.spm.spatial.preproc.opts.biasfwhm = 60;
> matlabbatch{3}.spm.spatial.preproc.opts.samp = 3;
> matlabbatch{3}.spm.spatial.preproc.opts.msk = {''};
> matlabbatch{3}.spm.tools.preproc8.warp.reg = 4;
> matlabbatch{3}.spm.tools.preproc8.warp.affreg = 'mni';
> matlabbatch{3}.spm.tools.preproc8.warp.samp = 3;
> matlabbatch{3}.spm.tools.preproc8.warp.write = [0 0];
>
>
> And this is the batch that I replaced and previously generated rc1*:
>
> % matlabbatch{3}.spm.tools.preproc8.channel.vols = {ref};
> % matlabbatch{3}.spm.tools.preproc8.channel.biasreg = 0.0001;
> % matlabbatch{3}.spm.tools.preproc8.channel.write = [0 0];
> % % matlabbatch{3}.spm.tools.preproc8.tissue(1).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,1'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(1).tpm =
> {'/usr/local/spm8/tpm/grey.nii,1'};
> %
> % matlabbatch{3}.spm.tools.preproc8.tissue(1).ngaus = 2;
> % matlabbatch{3}.spm.tools.preproc8.tissue(1).native = [1 1];
> % matlabbatch{3}.spm.tools.preproc8.tissue(1).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(2).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,2'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(2).ngaus = 2;
> % matlabbatch{3}.spm.tools.preproc8.tissue(2).native = [1 1];
> % matlabbatch{3}.spm.tools.preproc8.tissue(2).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(3).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,3'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(3).ngaus = 2;
> % matlabbatch{3}.spm.tools.preproc8.tissue(3).native = [1 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(3).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(4).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,4'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(4).ngaus = 3;
> % matlabbatch{3}.spm.tools.preproc8.tissue(4).native = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(4).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(5).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,5'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(5).ngaus = 4;
> % matlabbatch{3}.spm.tools.preproc8.tissue(5).native = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(5).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(6).tpm =
> {'/usr/local/spm8/toolbox/Seg/TPM.nii,6'};
> % matlabbatch{3}.spm.tools.preproc8.tissue(6).ngaus = 2;
> % matlabbatch{3}.spm.tools.preproc8.tissue(6).native = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.tissue(6).warped = [0 0];
> % matlabbatch{3}.spm.tools.preproc8.warp.reg = 4;
> % matlabbatch{3}.spm.tools.preproc8.warp.affreg = 'mni';
> % matlabbatch{3}.spm.tools.preproc8.warp.samp = 3;
> % matlabbatch{3}.spm.tools.preproc8.warp.write = [0 0];
>
>
>
>
