Hey friends. I used to do 1st level and second level analysis using SPM matlab, but now I want to switch to Nipype. The tutorial on the official documentation is great, but I have a few questions: 1. how to include motion regressors? In matlab, the following two lines imports the motion regressors from the realignment step:
matlabbatch{2}.spm.stats.fmri_spec.sess(r).regress = struct(‘name’, {}, ‘val’, {});
matlabbatch{2}.spm.stats.fmri_spec.sess(r).multi_reg = {[‘fMRI_data_nifti/sub-’ subject ‘/func/run-’ run_id ‘/rp_sub’ subject ‘_run-’ run_id ‘_bold.txt’]};
2. In matlab, I need to put in the time point of the first functional slice and the total number of slices: matlabbatch{2}.spm.stats.fmri_spec.timing.fmri_t0, matlabbatch{2}.spm.stats.fmri_spec.timing.fmri_t. Nipype doesn’t seem to require that. Why?
3. When specifying contrast in SPM matlab, there is an option: matlabbatch{1}.spm.stats.con.consess{con}.tcon.sessrep = ‘replsc’; so that I don’t have to divide the contrast weightings by the number of runs. This would be convenient for me as I have motion regressor and different number of runs for different subjects. Is there a similar function in Nipype?
Thanks you so much for your time!