how to convert spm script to maatlab command codes?

hello

I have to preprocess about 50 subject in SPM toolbox so I want to convert the SPM script to matlab code so it done automatically insteasd of manually , i tried my best but it not working can you please help

thank you

%-----------------------------------------------------------------------
% Job saved on 28-Mar-2022 11:13:12 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------

% List of open inputs
nrun = 4; % enter the number of runs here
jobfile = {'/Users/RUN1 output/run1_job.m'};
jobs = repmat(jobfile, 1, nrun);
inputs = cell(0, nrun);
for crun = 1:nrun
end
spm('defaults', 'FMRI');
spm_jobman('run', matlabbatch);

% Execute the code specified in the SPM GUI

%%
matlabbatch{1}.spm.spatial.realign.estwrite.data = {
                                                    {
                                                    '/Users/1_005_fMRI_3_5mmvox_run1_20170119,1'
                                                    '/Users/1_006_fMRI_3_5mmvox_run2_20170119,1'
                                                    '/Users/1_007_fMRI_3_5mmvox_run3_20170119,1'
                                                    '/Users/1_008_fMRI_3_5mmvox_run4_20170119,1' 
                                                    }
                                                    }';
%%
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.sep = 4;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.interp = 2;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.weight = '';
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [2 1];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.interp = 4;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.mask = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.prefix = 'r';
matlabbatch{2}.spm.spatial.normalise.estwrite.subj.vol = {'mean.img,1'};
%%
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.biasreg = 0.0001;
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.biasfwhm = 60;
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.tpm = {'/Users/spm12/tpm/TPM.nii'};
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.affreg = 'mni';
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.fwhm = 0;
matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.samp = 3;
matlabbatch{2}.spm.spatial.normalise.estwrite.woptions.bb = [-78 -112 -70
                                                             78 76 85];
matlabbatch{2}.spm.spatial.normalise.estwrite.woptions.vox = [2 2 2];
matlabbatch{2}.spm.spatial.normalise.estwrite.woptions.interp = 4;
matlabbatch{2}.spm.spatial.normalise.estwrite.woptions.prefix = 'w';

%%
matlabbatch{3}.spm.spatial.smooth.data = {
                                          'wr.img,1'
                                          };
%%
matlabbatch{3}.spm.spatial.smooth.fwhm = [8 8 8];
matlabbatch{3}.spm.spatial.smooth.dtype = 0;
matlabbatch{3}.spm.spatial.smooth.im = 0;
matlabbatch{3}.spm.spatial.smooth.prefix = 's';

Answer 1

[Anurag]

Hi Mariam,

I understand that you want to convert your SPM batch script into a MATLAB script, refer to the following code automating the jobs:

% Set the number of runs
nrun = 4;
% Specify the path to the job file
jobfile = '/path_/to_/your_/job_file/run1_job.m';

% Loop through each run
for crun = 1:nrun    
    % Load the job file for each run
    load(jobfile);
    % Update the data input for each run
    matlabbatch{1}.spm.spatial.realign.estwrite.data = {
    {
    ['/Users/1_00' num2str(5 + crun) '_fMRI_3_5mmvox_run' num2str(crun) '_20170119,1']
    % Add paths for the other runs
    }
    }';
     
    % Execute the processing for this run
    spm('defaults', 'FMRI');
    spm_jobman('run', matlabbatch);
    % Clear matlabbatch to avoid interference with the next run
    
    clear matlabbatch;
    
end

Hope this helped.

Regards,

Anurag

[Mariam Alabbad]

thank you