Hi Freesurfer experts I recently created surfaces with recon-all, and found that in the straight gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping between the hemispheres. I have attached a picture to show the problem. You can see from the picture that the pial surface from the Right hemisphere (in Blue) and the pial surface from the left hemisphere ( in Red) are overlapping (crossing over) to the other hemisphere. how can I fix this? Thanks Jon
Hi Jon
that's pretty bad. Is the aseg also incorrect there? If so, try correcting it and rerunning
cheers Bruce On Mon, 21 Oct 2013, Jon Wieser wrote:
Hi Freesurfer experts I recently created surfaces with recon-all, and found that in the straight gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping between the hemispheres. I have attached a picture to show the problem. You can see from the picture that the pial surface from the Right hemisphere (in Blue) and the pial surface from the left hemisphere ( in Red) are overlapping (crossing over) to the other hemisphere. how can I fix this? Thanks Jon
HI bruce thanks for the info the aseg was ok, except that the Right and Left cerebral cortex lables were in adjacent voxel in the region. I modified aseg.mgz so that they didn't touch. by eraseing some of the segmentation in the space between the hemispheres.
At which stage do I restart the recon-all? I think I should restart at -normalization2, since that that,s the next step after the aseg.mgz is created JOn
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, October 21, 2013 12:46:09 PM Subject: Re: [Freesurfer] Pial surface interhemispheric overlap
Hi Jon
that's pretty bad. Is the aseg also incorrect there? If so, try correcting it and rerunning
cheers Bruce On Mon, 21 Oct 2013, Jon Wieser wrote:
Hi Freesurfer experts I recently created surfaces with recon-all, and found that in the straight gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping between the hemispheres. I have attached a picture to show the problem. You can see from the picture that the pial surface from the Right hemisphere (in Blue) and the pial surface from the left hemisphere ( in Red) are overlapping (crossing over) to the other hemisphere. how can I fix this? Thanks Jon
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yes, I think you could probably run -autorecon2-cp -autorecon3, but I'm not positive On Mon, 21 Oct 2013, Jon Wieser wrote:
HI bruce thanks for the info the aseg was ok, except that the Right and Left cerebral cortex lables were in adjacent voxel in the region. I modified aseg.mgz so that they didn't touch. by eraseing some of the segmentation in the space between the hemispheres.
At which stage do I restart the recon-all? I think I should restart at -normalization2, since that that,s the next step after the aseg.mgz is created JOn
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, October 21, 2013 12:46:09 PM Subject: Re: [Freesurfer] Pial surface interhemispheric overlap
Hi Jon
that's pretty bad. Is the aseg also incorrect there? If so, try correcting it and rerunning
cheers Bruce On Mon, 21 Oct 2013, Jon Wieser wrote:
Hi Freesurfer experts I recently created surfaces with recon-all, and found that in the straight gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping between the hemispheres. I have attached a picture to show the problem. You can see from the picture that the pial surface from the Right hemisphere (in Blue) and the pial surface from the left hemisphere ( in Red) are overlapping (crossing over) to the other hemisphere. how can I fix this? Thanks Jon
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.
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