Sure, try the bbregister tool

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Karan Desai
Sent: Tuesday, December 1, 2020 10:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Aligning functional and structural scans with FsFast

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Hi FreeSurfer developers,

I have Freesurfer anatomical data from recon-all, and pre-processed functional data in NifTI format from FSL and you would like to use FsFast to align that data. What would be the best way to do that using FsFast? Is this possible?

Thanks.