Thanks Bruce. Is there anyway to address it in the intensity normalization phase?
-----Original Message-----
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Feb 9, 2010 12:29 PM To: Sherri Novis echotalk@earthlink.net Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature
Hi Sherry,
that's pretty tough. The dura is very bright and quite close to the gm. You may need to erase more of the dura
Bruce
On Tue, 9 Feb 2010, Sherri Novis wrote:
Hello,
I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.)
I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0)
I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura).
Can you recommend any other flags or things to try before I edit/erase the excess by hand?
Thanks for your time - Sherri
Hi Sherri,
it's hard to say without seeing the images. If you want to send us the orig.mgz we can take a look. Can you also give us the details of the acquisition? Scanner, coil, TR/TE/flip/# of acquisitions, etc....?
Bruce On Tue, 9 Feb 2010, Sherri Novis wrote:
Thanks Bruce. Is there anyway to address it in the intensity normalization phase?
-----Original Message-----
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Feb 9, 2010 12:29 PM To: Sherri Novis echotalk@earthlink.net Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature
Hi Sherry,
that's pretty tough. The dura is very bright and quite close to the gm. You may need to erase more of the dura
Bruce
On Tue, 9 Feb 2010, Sherri Novis wrote:
Hello,
I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.)
I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0)
I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura).
Can you recommend any other flags or things to try before I edit/erase the excess by hand?
Thanks for your time - Sherri
Sheri, can you send the file to bruce via the file upload link:
https://www.nmr.mgh.harvard.edu/facility/filedrop/uploadauth.html
its too big to send as an attachment to the freesurfer list.
n.
On Tue, 2010-02-09 at 13:40 -0500, Bruce Fischl wrote:
Hi Sherri,
it's hard to say without seeing the images. If you want to send us the orig.mgz we can take a look. Can you also give us the details of the acquisition? Scanner, coil, TR/TE/flip/# of acquisitions, etc....?
Bruce On Tue, 9 Feb 2010, Sherri Novis wrote:
Thanks Bruce. Is there anyway to address it in the intensity normalization phase?
-----Original Message-----
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Feb 9, 2010 12:29 PM To: Sherri Novis echotalk@earthlink.net Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature
Hi Sherry,
that's pretty tough. The dura is very bright and quite close to the gm. You may need to erase more of the dura
Bruce
On Tue, 9 Feb 2010, Sherri Novis wrote:
Hello,
I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.)
I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0)
I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura).
Can you recommend any other flags or things to try before I edit/erase the excess by hand?
Thanks for your time - Sherri
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