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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.