Thank you Bruce.

Does freesurfer use any binary label map during any processing steps?

Best Regards, Sarina

________________________________________ 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, October 19, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip brains

Hi Sarina

the skull stripping is done by combining a deformable surface with a watershed algorithm not with a label mask. The volume brainmask.mgz can be used to specify what is in brain (voxels >5) and what is not in brain (voxels < 5)

cheers Bruce

On Wed, 19 Oct 2016, Karmacharya, Sarina wrote:

Dear Freesurfer team,

I have a questions for you regarding the binary masks (labels maps) that freesufer uses to skull strip the brain in the first part of recon-all.

I was wondering if freesurfer stores/saves this label mask that it uses to skullstrip? If so what would be the naming convention of this label map/mask and the location of the label map/mask in the freesurfer folder.

I will be waiting to hear back from you.

Best Regards, Sarina

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dear Bruce,

I needed the label maps for other registration purposes to run other software. So I was thinking if freesurfers outputs one I can use the same one instead of creating new ones.

Thanks for the suggestion and time, I will try to binarize the brainmask.

Thanks again

Best Regards, Sarina

________________________________________ 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, October 19, 2016 10:53 AM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip brains

sure, internally at times but most of the volumes we save have a bit more info than that. Is there some reason you need something to actually be binary? You could binarize the brainmask if you wanted

cheers Bruce

On Wed, 19 Oct 2016, Karmacharya, Sarina wrote:

Thank you Bruce.

Does freesurfer use any binary label map during any processing steps?

Best Regards, Sarina

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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, October 19, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip brains

Hi Sarina

the skull stripping is done by combining a deformable surface with a watershed algorithm not with a label mask. The volume brainmask.mgz can be used to specify what is in brain (voxels >5) and what is not in brain (voxels < 5)

cheers Bruce

On Wed, 19 Oct 2016, Karmacharya, Sarina wrote:

...

Dear Freesurfer team,

I have a questions for you regarding the binary masks (labels maps) that freesufer uses to skull strip the brain in the first part of recon-all.

I was wondering if freesurfer stores/saves this label mask that it uses to skullstrip? If so what would be the naming convention of this label map/mask and the location of the label map/mask in the freesurfer folder.

I will be waiting to hear back from you.

Best Regards, Sarina

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer