Hi David
if you upload a subject to our ftp site and give us enough detail to
replicate what you tried we will take a look
cheers
Bruce
On Fri, 10 Mar 2017, David
Semanek wrote:
Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
required a fair number of manual edits to the white matter volume in order
to correct defects in the white matter surface. Typically, these edits take
the form of removing voxels in the wm.mgz volume that have been incorrectly
identified as white matter, usually near the pial surface caused by
intensity artifacts resulting from motion. My experience in the past is that
generating the white matter surface after edits to the wm.mgz volume will
reliably change the geometry of the resulting surfaces.
However, on my current dataset, 1.5T adolescent brains with pervasive motion
artifacts that do not meet the threshold for unusable data, absolutely no
intervention I have done on the wm.mgz volume has any impact at all on the
generation of the white matter surfaces. I am really very puzzled by this.
All of the files that result from wm.mgz reflect the edits, however the aseg
does not.
The resulting white matter surfaces always follow the aseg white matter
definitions and never the wm.mgz edits. I feel as if there might be
something I am missing but this protocol has reliably been used to do white
matter edits in the past. I thought it may be an issue with fs 6 or the long
stream, but I have tried the same edits in 5.3, 6, long and cross streams
and nothing at all has worked.
Does anyone have any suggestions, or perhaps a hint that I am overlooking
something common?
Thanks,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
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