fMRI_pre-processing_modeling_ROI-analysis/step_08_segment_T1mean.m at main · jorennig/fMRI_pre-processing_modeling_ROI-analysis · GitHub

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%clear all
close all
clc

cf = pwd;

for i = 1:numel(sub)

    %% Native space
    results_dir_c = [cf '/POF_nifti/' sub{i}, filesep, 'T1'];

    t1_mean = dir(fullfile(results_dir_c, 'T1_mean.nii'));
    t1_mean = fullfile(results_dir_c, {t1_mean(:).name});

    matlabbatch = [];
    matlabbatch{1}.spm.spatial.preproc.channel.vols = t1_mean;
    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 = {'C:\Program Files\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 0];
    matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'C:\Program Files\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 = [1 0];
    matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'C:\Program Files\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 = [1 0];
    matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'C:\Program Files\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 = [1 0];
    matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'C:\Program Files\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 = [1 0];
    matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'C:\Program Files\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 = [1 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 = [0 0];

    % Run batch
    spm_jobman('run', matlabbatch);

end

clearvars -except sub