[Freesurfer] Pial and WM boundary edits
To whom it may concern, After running autorecon2 (recon-all -subjid -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File Save Volume. After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid ) however received an error that '-autorecon-pial' was not recognized. Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler -- Skyler G. Shollenbarger Graduate Student Clinical Psychology Neurospychology University of Wisconsin-Milwaukee ___ 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.
Re: [Freesurfer] Pial and WM boundary edits
Hi Skyler after adding control points one usually runs: recon-all -subjid subject -autorecon2-cp -autorecon3 cheers Bruce On Thu, 28 Jun 2012, Skyler Gabriel Shollenbarger wrote: To whom it may concern, After running autorecon2 (recon-all -subjid -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File Save Volume. After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid ) however received an error that '-autorecon-pial' was not recognized. Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler ___ 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.
