External Email - Use Caution
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 <lfol...@stanford.edu>
wrote:
> External Email - Use Caution
>
> 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
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Paul Wighton <
> p...@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 <lfol...@stanford.edu
> <mailto:lfol...@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
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu> <
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve <
> dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
> Sent: Monday, May 10, 2021 12:25 PM
> To: freesurfer@nmr.mgh.harvard.edu<mailto: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:
>
> External Email - Use Caution
>
> 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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