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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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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