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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