Hello,
I'm having troubles trying to obtain only the brain in T1-weighted RM images that contain metastases.
First of all I have converted the DICOM images to mgz with "mri_convert /usr/local/freesurfer/subjects/A0D0C0.dcm /usr/local/freesurfer/subjects/case1.mgz" . Then, I have employed "mri_watershed -atlas /usr/local/freesurfer/subjects/case1.mgz /usr/local/freesurfer/subjects/brainmaskcase1.mgz" but as I see with freeview, I obtain the original images with a really bad or any skull stripping. For example, in one case, the left part is removed a lot and the right is intact. I have lowered the threshold but nothing changes. How could I solve it?
I'm working in VirtualBox and I didn't find the ".license" file, so I haven't copied the three lines. Is it necessary?
Thank you very much
Regards,
Úrsula