I mean to run recon-all from the beginning. It looks like you tried to run just
the skull stripping, but it needs some files before that step
On 10/28/2019 4:17 PM, Adam Rytina wrote:
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Hello,
what do you mean by the beginning? You mean to download the tutorial set and
run recon-all on that?
Thanks
Adam
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Odesláno: pondělí 28. října 2019 15:34
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Předmět: Re: [Freesurfer] recon-all -skullstrip issues
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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