I see. I think you will be fine putting those through FS including
intensity normalization. Have you tried it?
cheers
Bruce
On Tue, 14 Jan 2020, Patrick wrote:
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Dear Prof. Glasser and Prof. Fischl,
Thank you for your reply. I have been given a
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Dear Prof. Glasser and Prof. Fischl,
Thank you for your reply. I have been given a set of bias corrected images
(probably using ANTs). The plan is to extract regional and whole brain volumes
for these T1-weighted images.
RegardsPatrick
On
I agree with Matt. We do multiple stages of bias correection to flatten
things out as much as possible. Can you give us an idea of what you are
trying to achieve?
On Mon, 13 Jan 2020, Glasser, Matthew wrote:
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Why do you want to do that?
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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: on behalf of Patrick
Reply-To: Patrick , Freesurfer support list
Date: Monday,
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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 -nonuintensitycor2) Running recon-all by
specifying "motioncor" followed
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That's it! Thank you Doug!
Best wishes,
Marina.
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Dear FreeSurfer experts,
I have two questions on subject IDs in FreeSurfer output.
1) is it possible to change to subject identifier in the FreeSurfer output
after recon-all has been run?
Background: I would like to upload data pre-processed with
