External Email - Use Caution        

Hello all,

I´m struggling with running "recon-all -skullstrip", in general with "recon-all". I added NIfTI series file to a new directory "QWE" (/usr/local/freesurfer/subjects/QWE) and running the skull stripping "mri_watershed /usr/local/freesurfer/subjects/QWE/ser.nii /usr/local/freesurfer/subjects/QWE/brainwithout.nii" without any proble.

However, when trying to adjust watershed parameters the problem occurs. "recon-all -skullstrip -wsthresh 5 -clean-bm -subjid QWE". There are afterwards some errors occuring: "mv: cannot stat '/usr/local/freesurfer/subjects/QWE/mri/brainmask.mgz': No such file or directory", "mghRead(/usr/local/freesurfer/subjects/QWE/mri/nu.mgz, -1): could not open file
mri_em_register: could not open input volume nu.mgz."

I´m working with image series "ser.nii" and "brainwithout.nii", not with "brainmask.mgz" and "nu.mgz" in the tutorial.

Please, where is the problem?

Thanks a lot

Adam

Bez virů. www.avast.com

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer