Hi Freesurfer experts, I asked this question yesterday. I ended up seeing that a similar question had been asked in July, and spoke to the asker of the question, who told me his problem had been zeroes on the control point dat file, for several points.
I have attempted to go back through these, and reran several subjects with such zeroes removed, however - the same problem reoccurs with the white matter surface being seen as the brain surface. Any help would be welcomed. Thank you. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel, Jennifer Lynn Sarai Sent: Wednesday, August 19, 2015 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface lines in manual edits Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-run. 1. A couple of the volumes initially had the white matter surface as the pial surface/cortical surface. Initially I tried running g-cut for some of the suggestions I found on the wiki when the surface lines are off. This didn't work on those problem volumes. 2. When editing with control points in order to get the white matter areas that were not incorporated into the white matter surface included, the control points have overcoverected and made the same issue that was the occurrence with the two or three original volumes - the white matter surface is seen as the brain/pial surface. I was conservative with these as well. I have been looking on the wiki for a way to adjust the actual surface lines manually based on the actual white matter/brain surface. I think this would be most useful, but I'm not sure if it is possible. If so, how could this be done - and, if not, what possible way of trouble shooting can help deal with this white matter as pial surface issue? Best regards, - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edu<mailto:jlk130...@utdallas.edu> ------------------------------------------------------------ I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein
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