Hello Freesurfer community,
1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me.
Command I am using: recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning
Please see attachments for before and after watershed images.
After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in.
2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error-
recon-all -skullstrip -clean-bm -gcut -subjid 10
ERROR: Flag -gcut unrecognized.
This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0
Thank you very much for your help.
Regards,
Sourav
Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce
On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Sourav
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems to be not working. However, our lab has used the watershed flag previously and it had worked. Not sure what has changed.
Thank you for your help.
Sourav
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, July 20, 2014 8:15 PM To: Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed
Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce
On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Sourav
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Hi Sourav
can you explain what failed? Was too much removed? Too little? What did you try to fix it? Bruce On Tue, 22 Jul 2014, SOURAV RANJAN KOLE wrote:
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems to be not working. However, our lab has used the watershed flag previously and it had worked. Not sure what has changed.
Thank you for your help.
Sourav
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, July 20, 2014 8:15 PM To: Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed
Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce
On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Sourav
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I do not see any improvement in the skull stripping by decreasing the height. I have also tried using the multistrip flag but I do not see any changes no matter the height. Also, it seems that after watershed, it is not respecting the manual edits that I have made as you can see in the Before_Watershed.png attachment in my first email.
Thank you for your help.
Sourav
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 22, 2014 5:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Watershed
Hi Sourav
can you explain what failed? Was too much removed? Too little? What did you try to fix it? Bruce On Tue, 22 Jul 2014, SOURAV RANJAN KOLE wrote:
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems to be not working. However, our lab has used the watershed flag previously and it had worked. Not sure what has changed.
Thank you for your help.
Sourav
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, July 20, 2014 8:15 PM To: Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed
Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce
On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Sourav
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Sourav
Can you explain exactly what you think is failing? Provide images in a couple of different views (coronal, sagittal) with arrows showing what you think is incorrect?
Cheers Bruce
On Jul 22, 2014, at 8:11 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Hi Bruce,
I do not see any improvement in the skull stripping by decreasing the height. I have also tried using the multistrip flag but I do not see any changes no matter the height. Also, it seems that after watershed, it is not respecting the manual edits that I have made as you can see in the Before_Watershed.png attachment in my first email.
Thank you for your help.
Sourav
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 22, 2014 5:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Watershed
Hi Sourav
can you explain what failed? Was too much removed? Too little? What did you try to fix it? Bruce
On Tue, 22 Jul 2014, SOURAV RANJAN KOLE wrote:
Hi Bruce,
Thank you for your message.
Yes, I rechecked the result and have tried it several times. It still seems to be not working. However, our lab has used the watershed flag previously and it had worked. Not sure what has changed.
Thank you for your help.
Sourav
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, July 20, 2014 8:15 PM To: Freesurfer support list Cc: greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed
Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce
On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE sourav.kole@utah.edu wrote:
Sourav
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-
Bruce Fischl -
SOURAV RANJAN KOLE