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 ________________________________ Od: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu za uživatele Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Odesláno: pondělí 28. října 2019 15:34 Komu: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 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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