Dear Mike,
You can use the files ending in  FSvoxelSpace.mgz for this. Or, when you use mri_convert, add the flags -rt nearest (for nearest neighbor interpolation) and -rl [targetFile] (resample like target file).
Cheers
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of M.M. Craig <mmc57@cam.ac.uk>
Sent: Sunday, October 23, 2016 2:53:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using hippocampal subfields in SPM
 
Hello All,

I have a question about using the hippocampal subfield segmentation.
I've got the subfields from the structural image using recon-all and now
I want to use the subfields as ROIs in SPM. I've tried using mri_convert
to convert the .mgz files to .nii. This works but it doesn't place the
subfields where they should be on the brain. Is there a command to
register the hippocampal subfield .mgz files to a structural image that
can be used in SPM? Thanks very much for your help.

Best wishes,
Mike
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