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

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Just a quick update, running `recon-all -all -s bert` inside `freesurfer/freesurfer:7.1.1` has already made it past the stage that is failing above on my machine.

-Paul

On Wed, May 26, 2021 at 4:24 PM Paul Wighton paul@corticometrics.com wrote:

That's very strange. The command that is failing seems to be:

mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
/usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform

But when I test running that in `freesurfer/freesurfer:7.1.1`, eg:

docker run -it --rm \
  -v ~/fs-license.txt:/fs-license.txt \
  -e FS_LICENSE=/fs-license.txt \
    freesurfer/freesurfer:7.1.1 \
      mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
/usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform

It works.

I'm running the full recon now:

docker run -it --rm \
  --platform linux/amd64 \
  -v ~/fs-license.txt:/fs-license.txt \
  -e FS_LICENSE=/fs-license.txt freesurfer/freesurfer:7.1.1 \
    recon-all -all -s bert

and can report back when that finishes.

Can you try running the single command (mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform) and share the output?

Another option would be to try a different container. I'm worried this may be a mac issue, but you could try `pwighton/freesurfer:7.1.1`, which is built using neurodocker and might install a slightly different set of packages.

-Paul

On Mon, May 17, 2021 at 1:21 PM Lara Foland-Ross lfoland@stanford.edu wrote:

...

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Hello,

I am using Freesurfer7.1.1 ("docker pull freesurfer/freesurfer:7.1.1").

The docker command I'm using is: docker run -it --platform linux/amd64 freesurfer_gui

Thanks, Lara

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From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Paul Wighton < paul@corticometrics.com> Sent: Tuesday, May 11, 2021 8:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

    External Email - Use Caution

Hi Lara,

What container are you using? Is it `freesurfer/freesurfer:7.1.1`? Can you share the docker run command you're using?

-Paul

On Mon, May 10, 2021 at 10:00 PM Lara Foland-Ross <lfoland@stanford.edu mailto:lfoland@stanford.edu> wrote: External Email - Use Caution

Sure. Here's the output:

sh-4.2# mri_info mri/rawavg.mgz Volume information for mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5.3997 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 133.3997 0.0000 0.0000 1.0000 -110.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 133.3997 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 110.0000 -0.0000 -0.0000 -0.0000 1.0000

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From: freesurfer-bounces@nmr.mgh.harvard.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve < dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Monday, May 10, 2021 12:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: 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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