Why do you want to do that? FreeSurfer pretty much requires the values to be uniform across the brain and be in a specified range to work properly.

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Patrick <cool_dead_unleashed@yahoo.com>
Reply-To: Patrick <cool_dead_unleashed@yahoo.com>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, January 13, 2020 at 5:44 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Skipping bias field correction

External Email - Use Caution

Dear Freesurfer experts,

I am trying to run recon-all but I want to skip bias field estimation and correction step. I have tried the following:

1) Run recon-all by specifiying -nonuintensitycor

2) Running recon-all by specifying "motioncor" followed by "talairach" (additionally copying "orig" file and renaming it as "nu"

However, in both the cases, it looks like Freesurfer is still running bias correction. How can I go about skipping bias field correction?

Thanks and Regards

Patrick

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