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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
https://secure-web.cisco.com/1yiv8vlZ3k9XL8VmPsKSFGBhQpV_d1CqNGmb1zm8XRsvfT3IM0DINYYDRQOyhKnWxV2zYkTvRevpEDkpJSUPX2UIz_g6YWkF_5uDZqIxO0NuMONwMlRd8wdVNYIRNnNRxtCWGvMh0n7SeQiWp0bu1sExRCHzBrEyAYzUVQ30xiiUf4pnngkeuPNRqljMcMN-TgCWP33MJ6S9haztQJSuz6lOFDdvsQMWEzx4Xa4u-VtjPyl9xMlkgmH1eV5B8Q5w1gpPoMScnypjrvc8bex67KA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1vIG1ZdnORPNRjlNyEUTpSJVMFgbMgXIajEG3mdnQjMUs0ou9_oAMIFh1YZQ_F0m3xV7cChPU83_yX5EaY_OeU77qDYjjgesjwVlsa9j9NqAjvmZz4HrnXIeWalHN6RjTSQkE6nFVxqnRBb543YZC867W9r9fMzI1nxkY_VBfPMRt7JGLK6QFFUaVwQGMz0WJXPGw7EsREGFrWq-hrwMFU1Jlod5-3hg02A5cCUnLSmnIfo28F9nd53tWeHR3tvlC1onFtqd9jQBKtyow4CuhYQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/10TnTtT22QmGp0dAU6ZNfHgSa_zuKM0ARwAnl8yv6dQG7-e402Z2C1cHn2d7rYNS2L17jt3aPlqtcKZv2A7kx1Azs07u1qtZMGu_ZBA_p8010aTTCwZb_fOe6qAMmhPaNC7paZvXFTKG1Ji13NpmWIuAGpE1Ldc4hCIJo3j0hq4mvEFIhKWlqZHlWKvitFfqajG2mO_QU0ocMssTQm3Bnh8b1S2ozz8yx7HSorY-ELdDN8OC6tCP5OgND6CnYGHYO5a0rq6OOSfSgRUhnxIswkA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
