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