Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it incorporate the stroke? Also, does it matter if it's a cortical stroke and i am using v6.0 and i don't see aseg.manedit.mgz.
Best, Paul
On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
try something like
mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz --segid 77
This will model the strokes as WM hypointensities
On 09/07/2017 11:54 AM, miracle ozzoude wrote:
Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all -autorecon2-noaseg -autorecon3.
I have done the first part:
- mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii
stroke.mgz (use freeview to check the accuracy)
I want to combine the stroke.mgz with the aseg.presurf.mgz in order to create a new ROI. what command should I use to accomplish this? Thanks
Best,
Paul
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