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ii_Normalise.m
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ii_Normalise.m
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%% Normalise individual structural scans and electric field magnitude images produced by ROAST
% (c) Carys Evans, UCL
% carys.evans@ucl.ac.uk
% October 2019
%This script requires SPM12
%To run this script, make sure you have run your current flow models
%through ROAST. This script converts structural MRI and E-field magnitude
%images generated by ROAST from native to standard space. This is necessary
%for any group-based statistical analysis on E-field data.
%% Define file names and locations
%FILE NAMES MUST MATCH THOSE USED IN ROAST MODELS
%Define folder path where MRI scans are located
%THIS WILL NEED TO BE CHANGED ON ANOTHER COMPUTER
root = 'C:\Users\cevans\Desktop\Data\';
%Define individual scans being normalised (e.g. subject1.nii), excluding
%file extension '.nii'. Scans need to be in the same folder.
subj = {'subject1', 'subject2', 'subject3', 'subject4', 'subject5', 'subject6', 'subject7', 'subject8',...
'subject9', 'subject10', 'subject11', 'subject12', 'subject13', 'subject14', 'subject15',...
'subject16', 'subject17', 'subject18', 'subject19', 'subject20', 'subject21', ...
'subject23', 'subject24', 'subject25', 'subject26', 'subject27', 'subject28', 'subject29',...
'subject30', 'subject31', 'subject32', 'subject33', 'subject34', 'subject35', 'subject36',...
'subject37', 'subject38', 'subject39', 'subject40', 'subject41', 'subject42', 'subject43',...
'subject44', 'subject45', 'subject46', 'subject47', 'subject48', 'subject49', 'subject50',...
'subject51', 'subject52', 'subject53'};
%Define tag used by ROAST to identify simulation
simtag = 'CP5FC1_1mA';
%Define file path for Tissue Probability Map used by SPM during
%normalisation. TPM.nii is found in spm folder: spm12\tpm\TPM.nii.
%THIS WILL NEED TO BE CHANGED ON ANOTHER COMPUTER
tpm = 'C:\Users\cevans\Documents\spm12\tpm\TPM.nii';
%% Normalise each individual's structural MRI and emag (E-field magnitude) image generated by ROAST
for i = 1:length(subj)
spm('defaults', 'FMRI');
cd(root)
spm_jobman('initcfg')
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.vol = {[root, sprintf('%s.nii', subj{i}),',1']};
matlabbatch{1}.spm.spatial.normalise.estwrite.subj.resample = {
[root, sprintf('%s.nii', subj{i}),',1'] %Normalise structural MR image
[root, sprintf('%s_%s_emag.nii', subj{i}, simtag),',1'] %Normalise emag (E-field magnitude) image
};
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.biasreg = 0.0001;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.biasfwhm = 60;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.tpm = {tpm}; %Location of Tissue Probability Map used in SPM
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.affreg = 'mni';
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.fwhm = 0;
matlabbatch{1}.spm.spatial.normalise.estwrite.eoptions.samp = 3;
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.vox = [1 1 1]; %Resampled to 1mm resolution. Nb: normalised images in Evans et al., 2020 are at 2x2x2mm resolution
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.interp = 4;
matlabbatch{1}.spm.spatial.normalise.estwrite.woptions.prefix = 'w'; %File prefix for Normalised images. Can be changed as desired
spm_jobman('run', matlabbatch);
end