Dear Freesurfer experts,
When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command.
Please advise me what I can do.
Many thanks,
Iwo Bohr, PhD School of Computing Science University of Newcastle, UK
Hi Iwo,
you do not say which command exactly you ran. brainmask is created in the "first" step of the processing pipeline, so to obtain it you should have successfully completed the following:
recon-all -autorecon1 -s YOUR_SUBJECT
Best,
Martin
On Thursday 28 May 2009 11:24:27 Iwo Bohr wrote:
Dear Freesurfer experts,
When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command.
Please advise me what I can do.
Many thanks,
Iwo Bohr, PhD School of Computing Science University of Newcastle, UK
were there any errors in the log? Try running it with -make all to have it rebuild missing files On Thu, 28 May 2009, Iwo Bohr wrote:
Dear Freesurfer experts,
When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command.
Please advise me what I can do.
Many thanks,
Iwo Bohr, PhD School of Computing Science University of Newcastle, UK
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Iwo Bohr -
Martin Kavec