I would reprocess all the way through first and see if the remaining dura
affects the surfaces, then only edit in those locations that it does
cheers
Bruce
On Wed, 29 Nov 2017, Boyd, Emma wrote:
Hi Arsenije,
If you've already tested out different watershed thresholds and gcut, then
yes, the next step would be to manually erase these voxels and reprocess.
The ventricle labeling is a separate problem - which version of FreeSurfer
are you running?
Best,
Emma
---------
Emma Boyd
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
____________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Arsenije Subotic
<arsenije.subot...@ucalgary.ca>
Sent: Tuesday, November 28, 2017 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Erroneous output after recon-all: Bad segmentation and
surfaces
Dear experts,
I recently finished processing a subject for whom I had performed a skull-st
rip on the brainmask.mgz volume. I decreased the watershed parameter and re-
examined
the brainmask and the portion of the skull was gone, although some dura was
left over. I did a recon-all using the following command as the troubleshoo
ting tutorial suggested to regenerate the surfaces based on the new brainmas
k.mgz volume:
recon-all -autorecon-pial -subjid <subject name>
However, after the subject finished processing the surfaces were generated/o
utlined on the dura as well. I tried performing a g-cut command but it did n
ot get rid of the dura. I also had issues with the subcortical segmentation
as the ventricles were not completely segmented.
I've attached screenshots for you to see as well. Would it be necessary to m
anually erase the extra dura and then re-process the subject? Please let me
know.
Thank you for your help.
Best,
Arsenije
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