Unable to run example data using Docker on Windows

[neuropil]

I am using an installation of mindboggle on Windows 10.

No matter how I set my PATHS in Docker, I am unable to run MindBoggle on the example data.

I have attempted to run mindboggle by directly indicating the location of the example data: :~# mindboggle C:\Users\DrJTHome\mindboggle_input_example\freesurfer\subjects\arno

I get the same error: ‘Please provide correct path to DATA’

Any help would be greatly appreciated.

[chrisgorgo]

Are you using:

docker run --rm -ti -v $PATH_ON_HOST:/root/data \
    --entrypoint /bin/bash bids/mindboggle;

To run mindboggle?

[neuropil]

I am. But now I'm getting a different error.

At line:2 char:24

• docker run --rm -ti -v $PATH_ON_HOST:/root/data \

• 
  Variable reference is not valid. ':' was not followed by a valid variable name character. Consider using ${} to
  delimit the name.
  At line:3 char:7

• --entrypoint /bin/bash bids/mindboggle;
• ~ Missing expression after unary operator '--'. At line:3 char:7
• --entrypoint /bin/bash bids/mindboggle;

• 
  Unexpected token 'entrypoint' in expression or statement.
  + CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
  + FullyQualifiedErrorId : InvalidVariableReferenceWithDrive

[chrisgorgo]

Is this powershell? Try doing it in a single line and without variables (replace $PATH_ON_HOST with its value).

On Mon, Mar 20, 2017 at 4:08 PM, John notifications@github.com wrote:

I am. But now I'm getting a different error.

At line:2 char:24

• docker run --rm -ti -v $PATH_ON_HOST:/root/data \

•               ~~~~~~~~~~~~~~

Variable reference is not valid. ':' was not followed by a valid variable name character. Consider using ${} to delimit the name. At line:3 char:7

-

--entrypoint /bin/bash bids/mindboggle;

-

 ~

Missing expression after unary operator '--'. At line:3 char:7

-

--entrypoint /bin/bash bids/mindboggle;

-

 ~~~~~~~~~~

Unexpected token 'entrypoint' in expression or statement.

• CategoryInfo : ParserError: (:) [], ParentContainsErrorRecordException
• FullyQualifiedErrorId : InvalidVariableReferenceWithDrive

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[neuropil]

Hello Chrisfilo,

Thank you for your help! I am using powershell. Should I use something else?

When I run the entire line (see below), I still get a 'variable' error. Which variables should I leave out? Also, do I need to run the lines '--entrypoint /bin/bash bids/mindboggle'? What is this referring to?

docker run --rm -ti -v $C:\Users\John :\root\data --entrypoint /bin/bash bids/mindboggle

[chrisgorgo]

Ty this instead

docker run --rm -ti -v C:\Users\John:\root\data --entrypoint /bin/bash bids/mindboggle

[binarybottle]

@neuropil -- Did @chrisfilo help to resolve this issue for you?

[binarybottle]

Have you had any success running Mindboggle on your Windows system yet? I have created a new Docker container that will run FreeSurfer, ANTs, and a revised Mindboggle. Please see the new docker pull and run instructions (http://mindboggle.readthedocs.io/en/latest/#installing-mindboggle).

[binarybottle]

@neuropil -- I have created a new Docker container that can be used to execute (FreeSurfer, ANTs, and) Mindboggle from the command line, without having to enter the bash shell inside the container. It now takes a single command to install and a single command to run (see http://mindboggle.readthedocs.io/en/latest/#installation). Please tell me if this resolves your issue.

[neuropil]

@binarybottle Thank you for updating the container and documentation. This issue can be closed, as it does not pertain to Mindboggle, but my lack of understanding on how to use Docker.

[cochrand]

Following the instructions at http://mindboggle.readthedocs.io/en/latest/, I get the following error in Windows 10

Create missing output directory /home/jovyan/work/mindboggle123_output Create missing working directory /home/jovyan/work/mindboggle123_output/working Traceback (most recent call last): File "/opt/conda/bin/mindboggle123", line 147, in reconall.inputs.T1_files = IMAGE File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 2043, in validate value = super(MultiPath, self).validate(object, name, newvalue) File "/opt/conda/lib/python3.5/site-packages/traits/trait_types.py", line 2337 , in validate return TraitListObject( self, object, name, value ) File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2 314, in init raise excp File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2 306, in init value = [ validate( object, name, val ) for val in value ] File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2 306, in value = [ validate( object, name, val ) for val in value ] File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/traits_extensio n.py", line 92, in validate self.info_text, value)) traits.trait_errors.TraitError: The trait 'T1_files' of a ReconAllInputSpec inst ance is an existing file name, but the path 'C:/Program Files/Git/home/jovyan/w ork/example_mri_data/T1.nii.gz' does not exist.

[PeerHerholz]

The above problem is referenced in it's own issue and can be followed here.