I don't think you want noaseg. Why not try autorecon2-cp so it starts
after the aseg but uses it?
cheers
Bruce
On Thu, 23 Apr 2015, Clara Kuehn wrote:
Hi Paul,
thanks for your reply. I think the problem is that after editing the aseg.mgz
and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the
surfaces still cross.
Cheers, Clara
----- Ursprüngliche Mail -----
Von: silve...@gmx.com
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 23. April 2015 03:24:51
Betreff: Re: [Freesurfer] crossing medial surfaces
Hi Clara,
The method for dealing with the crossing medial surfaces that works for me is
decribed in the email below. Though, I'm not sure if there are any issues or
concerns with this approach particularly in regard to thickness or the
segmentations.
Paul
Sent: Tuesday, October 22, 2013 at 9:49 AM
From: "silve...@gmx.com" <silve...@gmx.com>
To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] medial wall crossing the surface: repost
Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what
about the instances where the aseg is correct and the pial surfaces cross?
Other than needing to update aseg.stats, are there any other concerns with the
'hemisphere' approach I described below?
Thanks again,
Paul
----- Original Message -----
From: Bruce Fischl
Sent: 10/22/13 09:46 AM
To: silve...@gmx.com
Subject: Re: [Freesurfer] medial wall crossing the surface: repost
Try fixing the aseg and rerunning
Cheers
Bruce
On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" <silve...@gmx.com> wrote:
Not always, but yes, in some instances the aseg crosses.
----- Original Message -----
From: Bruce Fischl
Sent: 10/18/13 01:22 PM
To: silve...@gmx.com
Subject: Re: [Freesurfer] medial wall crossing the surface
Does the aseg cross as well?
On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" <silve...@gmx.com> wrote:
Dear All,
I too am seeing the medial pial surfaces crossing hemispheres in some subjects.
The approach that appears to be working for me involves making copies of
brainmask.mgz and aseg.mgz
For the left hemisphere crossing into the right, edit brainmask.mgz and
aseg.mgz to delete voxels at the crossing belonging to the right hemisphere.
I then run recon-all -autorecon-pial -hemi lh -subjid subject
followed by returning the brainmask.mgz and aseg.mgz back to their original
copy.
This is similarly repeated for the right hemisphere crossing into the left.
Are there any issues or concerns with this approach particularly in regard to
thickness or the segmentations?
Thanks,
Paul
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
