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> 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 < > 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 > > > > > _______________________________________________ > Freesurfer mailing list > 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 > https://secure-web.cisco.com/10TnTtT22QmGp0dAU6ZNfHgSa_zuKM0ARwAnl8yv6dQG7-e402Z2C1cHn2d7rYNS2L17jt3aPlqtcKZv2A7kx1Azs07u1qtZMGu_ZBA_p8010aTTCwZb_fOe6qAMmhPaNC7paZvXFTKG1Ji13NpmWIuAGpE1Ldc4hCIJo3j0hq4mvEFIhKWlqZHlWKvitFfqajG2mO_QU0ocMssTQm3Bnh8b1S2ozz8yx7HSorY-ELdDN8OC6tCP5OgND6CnYGHYO5a0rq6OOSfSgRUhnxIswkA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >
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