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segmentation.m
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segmentation.m
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function segmentation(subject_root_dir, filePrefix)
% expects prefix rar
run1_images = get_session_data(subject_root_dir, filePrefix);
matlabbatch{1}.spm.spatial.preproc.channel.vols = run1_images;
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,1'};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [1 1];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,2'};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,3'};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,4'};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,5'};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'G:\My Drive\Msc neuroscience\matlab packages\spm12\tpm\TPM.nii,6'};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [1 1];
matlabbatch{1}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{1}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
spm_jobman('run' , matlabbatch);
matlabbatch = [];