Data preparation

Setting up the directory structure

Neuroimaging experiments result in complicated data that can be arranged in many different ways. Historically, individuals have tended to use their own unique naming/directory structures. The “Brain Imaging Data Structure” (BIDS) Specification has been designed to standardise this to help others understand the data, aiding replication, data-sharing and collaborations. For more details see: https://bids.neuroimaging.io/

For this demo, we will use the anatomical and naming convention as per BIDS:

[some path]/spm_vbm_tutorial/start/sub-001/anat/

See the end of this section for a code snippit to combine this with dicom import.

DICOM import

Normally, MRI data comes from the scanner in dicom file format (.dcm). To use this we first need to import the data and convert it into nifti file format. It is preferable to use “single file nifti format” rather than two-file (.img and .hdr).

Dicom import is located on the main SPM menu:

This will open up a GUI, where you can select the .dcm data, output directory and output file format.

Obviously this could get a bit tedious with lots of data, so the easiest thing is to write a short section of code to do this. A really useful function in SPM is the View Show .m code:

This will open a window with the corresponding code for that function. You can then copy and paste it into your own script. Over is a short example for the data import. I have modified it a bit to restructure the data following BIDs.

%Modify naming as required:
study='vbmdemo/';%Study
group{1}='group-01/'; %subgroup1 - For simplicity with analysis
group{2}='group-02/'; %subgroup2

%Select path
OP=spm_select(1,'dir','Select path/location to build data directory');

%Some BIDS stuff
sub='sub-00n/';%subject numbering (N will be 1 -> max)
bidsanatomy='/anat/'; %bids anatomy format

X{1}=spm_select(inf,'dir','Directories containing GROUP1 .dcm');
X{2}=spm_select(inf,'dir','Directories containing GROUP2 .dcm');

for j=1:2
for i=1:size(X{j},1);
    target=char(strcat(OP,'/',study,group{j},sub(1:end-2),num2str(i),bidsanatomy));
    mkdir(target);
    clear matlabbatch
    %Select dicom data in directory
    data=spm_select('FPListRec',deblank(X{j}(i,:)),'.*.dcm');

    %This was copied from show .m code, and the variables above plugged in
    matlabbatch{1}.spm.util.import.dicom.data = cellstr(data);
    matlabbatch{1}.spm.util.import.dicom.root = 'flat';
    matlabbatch{1}.spm.util.import.dicom.outdir = cellstr(target);
    matlabbatch{1}.spm.util.import.dicom.protfilter = '.*';
    matlabbatch{1}.spm.util.import.dicom.convopts.format = 'nii';
    matlabbatch{1}.spm.util.import.dicom.convopts.icedims = 0;

    %Command to make matlabbatch run in spm
    spm_jobman('run',matlabbatch)

    %Now need to rename output to be consistent with BIDS
    NiiFile=spm_select('FPList',target,'.nii');
    newfilename=char(strcat(target,sub(1:end-2),num2str(i),'_T1w.nii'));
    movefile(NiiFile,newfilename);
end
end

clear X group sub bidsanatomy data matlabbatch target study