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There's a section in the manual on using Dartel. This would allow a basic batch job to be created via the user interface, which is easy to modify manually. The code is in spm12/toolbox/DARTEL Providing you can achieve good alignment between structural and functional data, then using Dartel to spatially normalise your fMRI sounds like a very reasonable thing to do - particularly if you are looking at subcortical or more primary cortical regions. The benefits for cortex where there is more folding variability are a bit less certain. Best regards, -John On 10 December 2015 at 10:06, Ben Crittenden <[log in to unmask]> wrote: > Hello SPMers, > > I'm trying to upgrade some of my old pre-processing scripts to make use of > the dartel normalisation method. > > I have successfully realigned, resliced, slice-time corrected, > co-registered the EPI with the subjects' raw anatomical and run the dartel > preprocessing procedure. > > Using the old normalisation method, spm_preproc, I would pass the output > to spm_prep2sn which would give me the the normalisation parameters (and > their inverse) which I could apply to the EPI data using spm_write_sn. > > For the dartel procedure I have used a batch script, so my knowledge of > the functions here are not as good. > > My question is: where in the dartel processing pipeline could I get the > spatial normalisation parameters similar to what are given by spm_prep2sn > so that I can use them with the EPIs, as I was doing before? Does this > sound like a reasonable thing to do? > > Thanks, > > Ben > > >