Hi David, first I think it makes sense to - replicate the problem in the regular (cross sectional) stream - then fix it there (if it exists) or look for it in long.
So you see the problem in the S02_t1 and S02_t2 also, right? Best, Martin > On 13 Mar 2017, at 16:55, David Semanek <seman...@nyspi.columbia.edu> wrote: > > Thanks, I have uploaded the cross and long stream processing from one subject > which requires numerous white matter edits to correct defects in the white > matter surfaces; the file is on the ftp server as dsemanek.zip. > > Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to > both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 > have been run on them, as well as the long folder for the first time point, > s02_t1.long.s02_base. > > It was in working with the rerun results of s02_t1.long.s02_base that I > noticed the white matter surfaces after being regenerated with the edited > wm.mgz did not reflect any of the edits. The easiest way to see this is to > load the wm.mgz with the white matter surfaces and scroll through the slices, > there are numerous areas where the contours of the white matter surfaces do > not follow the voxels of the wm.mgz volume, mostly near what should be > identified as hyperintense gray matter. I’m fairly certain the white matter > surfaces didn’t change at all after running autorecon2-wm with the wm.mgz > edits. > > Thanks for taking a look at our data. > > Best, > > 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. > > On 3/12/17, 4:13 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > 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 >> >> >> >> 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. 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