Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

Can you run mri_info  /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz

On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:

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Hello,

I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple chip with BigSur as the OSX.

To test out the installation, I ran recon-all on bert:

recon-all -all -s bert

The command quits with this error:

"ERROR: cannot determine file type for /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021"

I'm attaching the recon-all.log file.

Could you please advise on how to troubleshoot?

Many thanks, Lara

Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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