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 <fischl@nmr.mgh.harvard.edu> wrote ----

Yes



On Sep 16, 2012, at 6:13 PM, Darren Gitelman <d-gitelman@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 <fischl@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-gitelman@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.

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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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 properly
dispose of the e-mail.