The flag -autorecon2-noaseg seems to no longer be used in version 5.1.
i.e. ERROR: Flag -autorecon2-noaseg unrecognized.
For edits made to aseg.mgz, could you please let me know what recon-all flags
are recommended for version 5.1 for the case described in the email below?
Thanks.
---- On Sun, 16 Sep 2012 16:07:20 -0700 Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote ----
Yes
On Sep 16, 2012, at 6:13 PM, Darren Gitelman
<d-gitel...@northwestern.edu> wrote:
Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels
labels as ventricle (250) but that didn't solve the problem.
Do I edit the aseg.mgz file and just label it as none in this region?
Would I use the command
tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs
-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
When done do I run recon-all -autorecon2-noaseg -autorecon3?
Thanks,
Darren
On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Check the aseg and see if it was labeled ventricle (and make sure it really
isn't). You may need to edit the aseg
On Sep 16, 2012, at 5:19 PM, Darren Gitelman
<d-gitel...@northwestern.edu> wrote:
Hi
I have run into an issue that I'm not sure how to correct. What happens is
that in some subjects the surfaces don't seem to properly track sulci coming
off the medial part of temporo-occipital cortex. Please see green arrows on the
attached image.
In fact the tutorial on topological defects shows an image with a similar
issue, but fixing it is not discussed.
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFile&do=get&target=TopoafterBM.jpg
I have checked and these are sulci and not the occipital extent of the lateral
ventricle.
Perhaps it is not a problem, or if it is then how to approach fixing it?
Thank you,
Darren
--
Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
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Darren Gitelman, MD
Northwestern University
710 N. Lake Shore Dr.
Abbott 11th Floor
Chicago, IL 60611
Ph: (312) 908-8614
Fax: (312) 908-5073
_______________________________________________
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contains patient information, please contact the Partners Compliance HelpLine
at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and
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