Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject then.

Thanks! Batool

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 14, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment

Hi Batool

if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least

cheers Bruce

On Wed, 14 Dec 2016, Rizvi, Batool wrote:

Hi FreeSurfer experts,

We have a subject on which we had to do adjust the watershed parameters for, since there was some brain missing from the brainmask.mgz. The watershed itself worked, but after that, we needed to regenerate the surfaces after the bad skull strip was fixed, and we ran "recon-all -autorecon-pial -subjid <subject name>"

That seemed to not work though, and it still shows that the surfaces do not include the new brain matter. Attached is an image of the output. Is there anything else we can try to regenerate these surfaces correctly?

Thank you!

Batool

not without more information. If you upload the tar and gzipped subject directory and give us a set of voxel coords that you want us to look at we will take a look

cheers Bruce On Wed, 14 Dec 2016, Rizvi, Batool wrote:

Hi Bruce,

Running -autorecon2 -autorecon3 did not seem to fix the surfaces for this subject. Do you have any further suggestions on what we could try to correct the surfaces?

Thank you! Batool

---

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool [br2499@cumc.columbia.edu] Sent: Wednesday, December 14, 2016 1:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment

Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3 on this subject then.

Thanks! Batool

---

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 14, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment

Hi Batool

if you need to change the watershed you will need to rerun everything from there forward. All of autorecon2 and autorecon3 I think at least

cheers Bruce

On Wed, 14 Dec 2016, Rizvi, Batool wrote:

...

Hi FreeSurfer experts,

We have a subject on which we had to do adjust the watershed parameters for, since there was some brain missing from the brainmask.mgz. The watershed itself worked, but after that, we needed to regenerate the surfaces after the bad skull strip was fixed, and we ran "recon-all -autorecon-pial -subjid <subject name>"

That seemed to not work though, and it still shows that the surfaces do not include the new brain matter. Attached is an image of the output. Is there anything else we can try to regenerate these surfaces correctly?

Thank you!

Batool

---

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