Re: [Freesurfer] automatically save the selected plane

External Email - Use Caution Hello My purpose is to get the specific(required) plane of axial view that lies in the midbrain region. For that i m thinking firstly to get all the planes of axial view from the midbrain region and then choose the best plane.i want to get the mickey m

Re: [Freesurfer] surf2vol ERROR

Oh I just used that option instead of providing a registration file, which I don't have. I need to turn the two surfaces into a single volume. Get Outlook for Android From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl

Re: [Freesurfer] surf2vol ERROR

Hi Vale mri_surf2vol is to take take from the surface to the volume within one subject. Why do you need a trgsubject? You can compute the registration with e.g. bbregister. Maybe I'm not understanding what you are trying to do cheers Bruce On Sat, 16 Feb 2019, Barletta, Valeria wrote:

[Freesurfer] Extracting stats from palm results (.mgz)

External Email - Use Caution Hi all, Do you have any suggestions on how I could extract stats (e.g., thickness, area, LGI, etc.) from a cluster(s) identified via palm? I've tried mri_label2label in order to turn the palm output .mgz into a paint .label file, but mri_label2label ca

[Freesurfer] surf2vol ERROR

Dear all, I am trying to register surfaces to a volume by this command: mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh --hemi lh --surfval lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge combined-CL.nii.gz --trgsubj MS089_R01_29 And am obtainin

[Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

External Email - Use Caution Dear Douglas, I wanted just to compute rescaled PET image without any PVC but following the same process as if I would have applied PVC. Moreover, I didn’t want to reduce FOV with auto mask generated (to still be in the gtmseg space). So I ran the f

Re: [Freesurfer] Fix topology correcting defect

Hi Yi-Fang the topology fixing time complexity is square in the convex hull of the largest defect. So small defects are quick and big ones take forever. That said, for any defects that can be fixed reliably the run time isn't too bad. Almost always if it is taking this long it means something