Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

2021-05-26 Thread Paul Wighton
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

2021-05-26 Thread Paul Wighton
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

2021-05-17 Thread Lara Foland-Ross
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




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Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

2021-05-11 Thread Paul Wighton
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
>
>
>
>
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Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

2021-05-10 Thread Lara Foland-Ross
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




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Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

2021-05-10 Thread Douglas N. Greve

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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