fMRI data preprocessing¶
Bringing it all together - scripting¶
If you are processing data from multiple subjects or sessions, you might want to automate your preprocessing pipeline by writing a script. This can speed up your data processing and ensure that each datapoint has been processed with the same parameters.
To start your script we will use the _job.m file generated when we saved the batch we put together in the previous tutorial on the batch interface.
First, open this your preprocessing_batch_job.m file in MATLAB and inspect its contents. It should look something like this:
%-----------------------------------------------------------------------
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.spatial.realign.estwrite.data = {{'/Users/spm/spm_tutorials/preprocessing/MoAEpilot/sub-01/func/sub-01_task-auditory_bold.nii'}};
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 = [0 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.temporal.st.scans{1}(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));
matlabbatch{2}.spm.temporal.st.nslices = 64;
matlabbatch{2}.spm.temporal.st.tr = 7;
matlabbatch{2}.spm.temporal.st.ta = 6.890625;
matlabbatch{2}.spm.temporal.st.so = [64 63 62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1];
matlabbatch{2}.spm.temporal.st.refslice = 32;
matlabbatch{2}.spm.temporal.st.prefix = 'a';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{3}.spm.spatial.coreg.estimate.source = {'/Users/spm/spm_tutorials/preprocessing/MoAEpilot/sub-01/anat/sub-01_T1w.nii,1'};
matlabbatch{3}.spm.spatial.coreg.estimate.other = {''};
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{4}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Coregister: Estimate: Coregistered Images', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','cfiles'));
matlabbatch{4}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{4}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{4}.spm.spatial.preproc.channel.write = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(1).tpm = {'/Applications/spm12/tpm/TPM.nii,1'};
matlabbatch{4}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).tpm = {'/Applications/spm12/tpm/TPM.nii,2'};
matlabbatch{4}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).tpm = {'/Applications/spm12/tpm/TPM.nii,3'};
matlabbatch{4}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).tpm = {'/Applications/spm12/tpm/TPM.nii,4'};
matlabbatch{4}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{4}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).tpm = {'/Applications/spm12/tpm/TPM.nii,5'};
matlabbatch{4}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{4}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).tpm = {'/Applications/spm12/tpm/TPM.nii,6'};
matlabbatch{4}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{4}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{4}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{4}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{4}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{4}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{4}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{4}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{5}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Slice Timing: Slice Timing Corr. Images (Sess 1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
matlabbatch{5}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{5}.spm.spatial.normalise.write.woptions.vox = [3 3 3];
matlabbatch{5}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{5}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{6}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
matlabbatch{6}.spm.spatial.smooth.fwhm = [6 6 6];
matlabbatch{6}.spm.spatial.smooth.dtype = 0;
matlabbatch{6}.spm.spatial.smooth.im = 0;
matlabbatch{6}.spm.spatial.smooth.prefix = 's';
We will now add a for loop around this script. This will tell SPM to perform the same operation on all datasets that we specify in our loop.
The basic structure of a for loop in MATLAB is:
We will now use this structure to ask SPM to perform all preprocessing steps specified in our batch file on all selected datasets:
clear all % clear all variables
clc % clear command window
root = '/Users/spm/spm_tutorials/preprocessing/MoAEpilot/' % specify the directory where your data lives
sub = {'sub-01'} % specify a list of subjects you want to process
% this loop will perform preprocessing steps for all subjects specified in the list sub
for i = 1:numel(sub)
disp(['Starting preprocessing for ', sub{i}]) % add a print statement to tell you which subject is being processed
anat_dir = fullfile(root, sub{i}, 'anat') % this combines the root with a specific subject directory to create the full path to the folder containing anatomical data
func_dir = fullfile(root, sub{i}, 'func') % this combines the root with a specific subject directory to create the full path to the folder containing functional data
% find the structural file
anat = spm_select('FPList', anat_dir, '^sub-*.*_T1w.nii$') % this will return the full path (FP) to the T1 file from the anat directory
%find and select the functional data
func = spm_select('ExtFPList', func_dir, '^sub-*.*_task-auditory_bold.nii$', NaN) % this will give the full path to the task data, NaN will ensure you are loading all volumes present (i.e. consider the 4D file as a whole)
cd(func_dir) % move into the subject specific folder containing the functional data
matlabbatch{1}.spm.spatial.realign.estwrite.data {1} = cellstr(func); % point the batch to the func variable
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 = [0 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.temporal.st.scans{1}(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));
matlabbatch{2}.spm.temporal.st.nslices = 64;
matlabbatch{2}.spm.temporal.st.tr = 7;
matlabbatch{2}.spm.temporal.st.ta = 6.890625;
matlabbatch{2}.spm.temporal.st.so = [64 63 62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1];
matlabbatch{2}.spm.temporal.st.refslice = 32;
matlabbatch{2}.spm.temporal.st.prefix = 'a';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{3}.spm.spatial.coreg.estimate.source = cellstr(anat); % point the batch to the anat variable
matlabbatch{3}.spm.spatial.coreg.estimate.other = {''};
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{4}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Coregister: Estimate: Coregistered Images', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','cfiles'));
matlabbatch{4}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{4}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{4}.spm.spatial.preproc.channel.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.tissue(1).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,1')};
matlabbatch{4}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,2')};
matlabbatch{4}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,3')};
matlabbatch{4}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,4')};
matlabbatch{4}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{4}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,5')};
matlabbatch{4}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{4}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).tpm = {fullfile(spm('Dir'),'tpm','TPM.nii,6')};
matlabbatch{4}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{4}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{4}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{4}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{4}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{4}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{4}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{4}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{5}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Slice Timing: Slice Timing Corr. Images (Sess 1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
matlabbatch{5}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{5}.spm.spatial.normalise.write.woptions.vox = [3 3 3];
matlabbatch{5}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{5}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{6}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
matlabbatch{6}.spm.spatial.smooth.fwhm = [6 6 6];
matlabbatch{6}.spm.spatial.smooth.dtype = 0;
matlabbatch{6}.spm.spatial.smooth.im = 0;
matlabbatch{6}.spm.spatial.smooth.prefix = 's';
disp(['Completed preprocessing for ', sub{i}]) % add a print statement telling you which subject has been processed
save preprocessing_batch matlabbatch % save the setup into a matfile called preprocessing_batch.mat
spm_jobman('run',matlabbatch) % execute the batch
clear matlabbatch % clear matlabbatch
end