Dear Freesurfer users,
My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated).
Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced!
Veronica
Hi Min, We've learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2 and see if it fixes everything. Allison
On Thu, 31 Mar 2011, Min Liu wrote:
Dear Freesurfer users,
My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated).
Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced!
Veronica
Dear Freesurfer users,
Thank you Dr.Stevens for suggestions. I reran -autorecon2 but still it didn't fix the pial surface. I edited wm.mgz again by adding more control points AND more white matter voxels using the 'edit voxel brush' but still, after reran the whole second recon step, pial surface failed to include the added wm voxels in. Pls see the attachment. Does anyone encounter the same thing before? Thank you for advice!
Min
On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens < astevens@nmr.mgh.harvard.edu> wrote:
Hi Min, We've learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2 and see if it fixes everything. Allison
On Thu, 31 Mar 2011, Min Liu wrote:
Dear Freesurfer users,
My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated).
Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced!
Veronica
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.
Hi Min, It's difficult to tell what may be going wrong based on that one slice. Could you upload the subject and send it to Khoa so she can investigate? She's an expert in exactly these kinds of problems. Allison
On Mon, 4 Apr 2011, Min Liu wrote:
Dear Freesurfer users,
Thank you Dr.Stevens for suggestions. I reran -autorecon2 but still it didn't fix the pial surface. I edited wm.mgz again by adding more control points AND more white matter voxels using the 'edit voxel brush' but still, after reran the whole second recon step, pial surface failed to include the added wm voxels in. Pls see the attachment. Does anyone encounter the same thing before? Thank you for advice!
Min
On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens < astevens@nmr.mgh.harvard.edu> wrote:
Hi Min, We've learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2 and see if it fixes everything. Allison
On Thu, 31 Mar 2011, Min Liu wrote:
Dear Freesurfer users,
My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated).
Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced!
Veronica
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@nmr.mgh.harvard.edu
-
Allison Stevens -
Min Liu