Hi Padma,

You can use the --like flag of mri_convert to convert the output of the skull stripping back to the dimensions of the original file

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert

e.g

mri_convert --like input-to-skullstrip.mgz output-from-skullstrip.mgz skullstripped_orig_dims.mgz

-Paul

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of priya padma <priya@phenomx.ai>
Sent: Thursday, October 27, 2022 3:05 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] change in mask size

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Dear Team,

I tried using freesurfer for skull stripping and I got results all of size 256X256X256 but the original data size is different, it's 512X512X537.

Is there any way to bring back the original size in freesurfer?

Any help would be appreciated.

Thank you

Best Regards

Padma Priya

AI Developer

PhenoMx, Inc.

priya@phenomx.ai | (+82)10-5405-2685