Did you run recon-all from the beginning? It needs to create those files
On 10/27/19 3:18 PM, Adam Rytina wrote:
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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
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