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
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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. 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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