Hi Sita,
Thanks for all the responses! I've actually had the same problem for multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. I've attached pictures of where I am adding wm voxels. They aren't really in the same places as in the online tutorials. Could you take a quick look to see if they're in the right place?
Thanks, Allie
On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:
Hi Allie,
pial surface which looks like this can only be corrected by correcting the wm.mgz. Also I would suggest to try and fix the cerebellum and see if it corrects the surfaces as well. Since part of the cerebellum is stripped off, it's probably affecting the segmentation as well but I could be wrong. what version of freesurfer are you using.
Sita.
On Mon, 18 Apr 2011, Allie Rosen wrote:
Hi Sita,
Can I still add voxels to wm.mgz even though the points would be outside even the pial boundary?
Thanks Allie
On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:
Hi Allie,
This probably needs white matter edits but it's hard to tell from one slice. Please refer to our white matter edits wiki and toplogical defects wiki and see if it helps in fixing the errors in your datasets. Also it looks like part of the Cerebellum is stripped off. You might want to correct that as well.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
Sita.
On Mon, 18 Apr 2011, Allie Rosen wrote:
Hi,
Once processed, several of my subjects have had errors around the occipital lobe. Attached is an example. I've already tried editing brainmask.mgz and running recon-all, but as you can see, this didn't change the pial or wm borders. What can I do to fix this?
Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto
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