External Email - Use Caution
Hi expert,
I found an issue when I do skull stripping. I used the following command line.
recon-all \
-skullstrip \
-s fs_output \
-clean-bm \
-wsthresh 100
But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed).
Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks.
PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots?
Best,
Cain
External Email - Use Caution
Hi Cain
Have you tried using mri_synthstrip instead?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of DS Sent: Sunday, August 6, 2023 3:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Bad skull stripping
External Email - Use Caution
Hi expert,
I found an issue when I do skull stripping. I used the following command line.
recon-all \
-skullstrip \
-s fs_output \
-clean-bm \
-wsthresh 100
But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed). Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks.
PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots?
Best,
Cain
External Email - Use Caution
Hi Bruce, Thanks for your reply. That's awesome. I just now tried mri_synthstrip, it works very well. I have another question. I first run recon-all and constructed the cortical surface. But, I found an issue of skull stripping, which caused the incorrect brainmask.mgz. Now this issue has been fixed. How can I regenerate the FreeSurfer output based on the new brainmask.mgz. Can I use the following command line to rerun it? Do I need to specify any other items? recon-all \ -autorecon-pial \ -subjid <subject name>
Thanks, Cain
At 2023-08-07 05:22:33, "Fischl, Bruce R.,PHD" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
Hi Cain
Have you tried using mri_synthstrip instead?
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of DS Sent: Sunday, August 6, 2023 3:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Bad skull stripping
External Email - Use Caution
Hi expert,
I found an issue when I do skull stripping. I used the following command line.
recon-all \
-skullstrip \
-s fs_output \
-clean-bm \
-wsthresh 100
But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed).
Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks.
PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots?
Best,
Cain
External Email - Use Caution
Hi Cain
If some brain was stripped I think you need to run all of autorecon2 and autorecon3
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of DS Sent: Sunday, August 6, 2023 8:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bad skull stripping
External Email - Use Caution Hi Bruce, Thanks for your reply. That's awesome. I just now tried mri_synthstrip, it works very well. I have another question. I first run recon-all and constructed the cortical surface. But, I found an issue of skull stripping, which caused the incorrect brainmask.mgz. Now this issue has been fixed. How can I regenerate the FreeSurfer output based on the new brainmask.mgz. Can I use the following command line to rerun it? Do I need to specify any other items? recon-all \ -autorecon-pial \ -subjid <subject name>
Thanks, Cain
At 2023-08-07 05:22:33, "Fischl, Bruce R.,PHD" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
External Email - Use Caution Hi Cain
Have you tried using mri_synthstrip instead?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Sunday, August 6, 2023 3:34 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Bad skull stripping
External Email - Use Caution
Hi expert,
I found an issue when I do skull stripping. I used the following command line.
recon-all \
-skullstrip \
-s fs_output \
-clean-bm \
-wsthresh 100
But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed). Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks.
PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots?
Best,
Cain
freesurfer@nmr.mgh.harvard.edu
-
DS -
Fischl, Bruce R.,PHD