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Hi Nathan,
are you sure that the SPM segmentation and the wm.mgz share the same space? You could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz
Best,
Falk
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Nathan Kindred (PGR) N.Kindred1@newcastle.ac.uk Gesendet: Mittwoch, 19. Januar 2022 13:29:46 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Using SPM segmentations in FreeSurfer
External Email - Use Caution Hi,
I have been trying to incorporate segmentation files from SPM into FreeSurfer to improve the surfaces, but I am not sure if I am going about it in the right way. I have been replacing the wm.mgz file with a file from SPM and then running ‘recon-all -s ${subject} -autorecon2-wm -autorecon3’, but I keep getting errors. I have tried using both conform and conform_min as part of mri_convert when replacing the wm.mgz file with an SPM file but in both cases I still get errors.
Are there other steps I should be taking or a different line of code I should run to get this to work?
Thanks, Nathan