Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
External Email - Use Caution Just a quick update, running `recon-all -all -s bert` inside `freesurfer/freesurfer:7.1.1` has already made it past the stage that is failing above on my machine. -Paul On Wed, May 26, 2021 at 4:24 PM Paul Wighton wrote: > That's very strange. The command that is failing seems to be: > ``` > mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz > /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform > ``` > > But when I test running that in `freesurfer/freesurfer:7.1.1`, eg: > ``` > docker run -it --rm \ > -v ~/fs-license.txt:/fs-license.txt \ > -e FS_LICENSE=/fs-license.txt \ > freesurfer/freesurfer:7.1.1 \ > mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz > /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform > ``` > It works. > > I'm running the full recon now: > ``` > docker run -it --rm \ > --platform linux/amd64 \ > -v ~/fs-license.txt:/fs-license.txt \ > -e FS_LICENSE=/fs-license.txt freesurfer/freesurfer:7.1.1 \ > recon-all -all -s bert > ``` > and can report back when that finishes. > > Can you try running the single command (mri_convert > /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz > /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform) and share the > output? > > Another option would be to try a different container. I'm worried this > may be a mac issue, but you could try `pwighton/freesurfer:7.1.1`, which is > built using neurodocker and might install a slightly different set of > packages. > > -Paul > > On Mon, May 17, 2021 at 1:21 PM Lara Foland-Ross > wrote: > >> 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 > <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: 1.00, 1.00, 1.00 >> 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: 0.00 >> ras xform present >> xform info: x_r = -1., y_r = 0., z_r = 0., c_r = >> 5.3997 >> : x_a = 0., y_a = 0., z_a = 1., c_a = >> 18. >> : x_s = 0., y_s = -1., z_s = 0., c_s = >> 0. >> >> talairach xfm : >> Orientation : LIA >> Primary Slice Direction: coronal >> >> voxel to ras transform: >>-1. 0. 0. 133.3997 >> 0. 0. 1. -110. >> 0. -1. 0. 128. >> 0. 0. 0. 1. >> >> voxel-to-ras determinant -1 >> >> ras to voxel transform: >>-1. -0. -0. 133.3997 >> -0.0000 -0.0000 -1. 128. >> -0. 1. -0. 110. >>-0. -0. -0. 1. >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu> freesurfer-boun...@nmr.mgh.harvard.edu> < >> freesurfer-boun...@nmr.mgh.harvard.edu> freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve < >> dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
External Email - Use Caution That's very strange. The command that is failing seems to be: ``` mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform ``` But when I test running that in `freesurfer/freesurfer:7.1.1`, eg: ``` docker run -it --rm \ -v ~/fs-license.txt:/fs-license.txt \ -e FS_LICENSE=/fs-license.txt \ freesurfer/freesurfer:7.1.1 \ mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform ``` It works. I'm running the full recon now: ``` docker run -it --rm \ --platform linux/amd64 \ -v ~/fs-license.txt:/fs-license.txt \ -e FS_LICENSE=/fs-license.txt freesurfer/freesurfer:7.1.1 \ recon-all -all -s bert ``` and can report back when that finishes. Can you try running the single command (mri_convert /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/freesurfer/subjects/bert/mri/orig.mgz --conform) and share the output? Another option would be to try a different container. I'm worried this may be a mac issue, but you could try `pwighton/freesurfer:7.1.1`, which is built using neurodocker and might install a slightly different set of packages. -Paul On Mon, May 17, 2021 at 1:21 PM Lara Foland-Ross wrote: > 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 <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: 1.00, 1.00, 1.00 > 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: 0.00 > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > 5.3997 > : x_a = 0., y_a = 0., z_a = 1., c_a = > 18. > : x_s = 0., y_s = -1., z_s = 0., c_s = > 0. > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 133.3997 > 0. 0. 1. -110. > 0. -1. 0. 128. > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. -0. -0. 133.3997 >-0. -0. -1. 128. >-0. 1. -0. 110. >-0. -0. -0. 1. > > > From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu> < > freesurfer-boun...@nmr.mgh.harvard.edu 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/
Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
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 on behalf of Paul Wighton 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 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: 1.00, 1.00, 1.00 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: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 5.3997 : x_a = 0., y_a = 0., z_a = 1., c_a =18. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 133.3997 0. 0. 1. -110. 0. -1. 0. 128. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 133.3997 -0. -0. -1. 128. -0. 1. -0. 110. -0. -0. -0. 1. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve 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%2Ff
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 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: 1.00, 1.00, 1.00 > 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: 0.00 > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > 5.3997 > : x_a = 0., y_a = 0., z_a = 1., c_a = > 18. > : x_s = 0., y_s = -1., z_s = 0., c_s = > 0. > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 133.3997 > 0. 0. 1. -110. > 0. -1. 0. 128. > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. -0. -0. 133.3997 >-0. -0. -1. 128. >-0. 1. -0. 110. >-0. -0. -0. 1. > > > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
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: 1.00, 1.00, 1.00 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: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 5.3997 : x_a = 0., y_a = 0., z_a = 1., c_a =18. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 133.3997 0. 0. 1. -110. 0. -1. 0. 128. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 133.3997 -0. -0. -1. 128. -0. 1. -0. 110. -0. -0. -0. 1. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.