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 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-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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

https://secure-web.cisco.com/1yiv8vlZ3k9XL8VmPsKSFGBhQpV_d1CqNGmb1zm8XRsvfT3...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10TnTtT22QmGp0dAU6ZNfHgSa_zuKM0ARwAnl8yv6dQG7-e...