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
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 mjalbrzikowski@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
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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 mjalbrzikowski@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@nmr.mgh.harvard.edu
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Maria Jalbrzikowski -
Michael Harms -
Tetiana Dadakova