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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 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 RegardsPatrick
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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: 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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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:
External Email - Use Caution
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:
Run recon-all by specifiying -nonuintensitycor
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
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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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 Tuesday, January 14, 2020, 6:45:20 AM GMT+5:30, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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:
External Email - Use Caution
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:
Run recon-all by specifiying -nonuintensitycor
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
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
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.
Regards Patrick
On Tuesday, January 14, 2020, 6:45:20 AM GMT+5:30, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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:
External Email - Use Caution
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:
Run recon-all by specifiying -nonuintensitycor
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
_
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you
are
not the intended recipient, be advised that any unauthorized use,
disclosure,
copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in
error,
please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Glasser, Matthew -
Patrick