Re: [Freesurfer] Bbregister misalignment {Disarmed}

You can ignore that warning. The source of the problem is that the whole-brain and the partial FoV are not in alignment. The idea here is that you acquire the whole head and the partial fov in the same scanning session so that they are more-or-less in alignment. When you register the whole brai

Re: [Freesurfer] Bbregister misalignment {Disarmed}

A couple of things to try: First, make sure that the whole head and the partial FoV EPIs are in register without doing any registration tkregisterfv --mov partialfovepi.nii.gz --targ wholeepi.nii.gz --regheader --reg partial-to-full.lta Next, register the whole head EPI to the structural bbr

[Freesurfer] mri_watershed

External Email - Use Caution Dear Freesurfer community, I have a question regarding the mri_watershed. Is the inner_skull extracted from the brain.mgz which gets masked by the brainmask.mgz automatically? Thanks ___ Freesurfer mailing

Re: [Freesurfer] Bbregister misalignment {Disarmed}

External Email - Use Caution Hi Doug, Thanks for this. However, I can’t seem to access the ftp: c1749990@l017:~/data/freesurfer/subjects$ ftp surfer.nmr.mgh.harvard.edu bash: ftp: command not found... Is there another way to do this? Cheers, Mason Mason T Wells, MSc PhD student