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 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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