Re: [Freesurfer] running recon-all after editing aseg.mgz
If you only made edits to the aseg, then you can run: recon-all -s subject_name -autorecon2-aseg -autorecon3 which omits some stages that don't need to be redone (but which would otherwise be included if you use the -autorecon2 flag). If you in addition added control points, then you would run recon-all -s subject_name -autorecon2-cp -autorecon3 which includes the stages needed to handle the aseg edits as well. cheers, -MH On Fri, 2011-11-25 at 22:49 +0100, Tetiana Dadakova wrote: Hi Maria, Yes, you are editing aseg.mgz. After saving the segmentation, you should run recon-all -s subject_name -autorecon2 -autorecon3. If you also added some control points, then you should run recon-all -s subject_name -autorecon2-cp -autorecon3 Best wishes, Tanja. On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (tkmedit your_subject_name brainmask.mgz -surfs -aseg) and use the edit the segmentation and then press save segmentation, I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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
[Freesurfer] running recon-all after editing aseg.mgz
Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (*tkmedit your_subject_name brainmask.mgz -surfs -aseg) * and use the edit the segmentation and then press save *segmentation, I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria *-- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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] running recon-all after editing aseg.mgz
Hi Maria, Yes, you are editing aseg.mgz. After saving the segmentation, you should run recon-all -s subject_name -autorecon2 -autorecon3. If you also added some control points, then you should run recon-all -s subject_name -autorecon2-cp -autorecon3 Best wishes, Tanja. On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (tkmedit your_subject_name brainmask.mgz -surfs -aseg) and use the edit the segmentation and then press save segmentation, I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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
