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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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The howto should be updated to also containing information about Ubuntu. #135

Closed knutj closed 6 years ago

knutj commented 6 years ago

The howto should be updated to also containing information about Ubuntu.

binarybottle commented 6 years ago

Do you mean how to use the installer script on Ubuntu rather than installing the Docker container, or how to install the Docker container on Ubuntu specifically?

binarybottle commented 6 years ago

Since I use Mindboggle on Ubuntu using the present instructions on the website, these instructions are based on my experience with Ubuntu. The top of the README (http://mindboggle.readthedocs.io/en/latest/) includes "We have tested the software most extensively with Python 3.5.1 on Ubuntu Linux 14.04"

I will close this issue, but if I have misunderstood you, please feel free to reopen it!

knutj commented 6 years ago

It would have been easier to understand if you had used docker that was installed with a packages from ubuntu. When I used host=/var/lib/docker DOCK=/home/jovyan/work # path to HOST from Docker container IMAGE=$DOCK/example_mri_data/T1.nii.gz # input image on HOST ID=arno # ID for brain image

I got this error docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle $IMAGE --id $ID Create missing output directory /home/jovyan/work/mindboggle123_output Create missing working directory /home/jovyan/work/mindboggle123_output/working Traceback (most recent call last): File "/opt/conda/bin/mindboggle123", line 147, in reconall.inputs.T1_files = IMAGE File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 2043, in validate value = super(MultiPath, self).validate(object, name, newvalue) File "/opt/conda/lib/python3.5/site-packages/traits/trait_types.py", line 2337, in validate return TraitListObject( self, object, name, value ) File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2314, in init raise excp File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2306, in init value = [ validate( object, name, val ) for val in value ] File "/opt/conda/lib/python3.5/site-packages/traits/trait_handlers.py", line 2306, in value = [ validate( object, name, val ) for val in value ] File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/traits_extension.py", line 92, in validate self.info_text, value)) traits.trait_errors.TraitError: The trait 'T1_files' of a ReconAllInputSpec instance is an existing file name, but the path '/home/jovyan/work/example_mri_data/T1.nii.gz' does not exist. [knutjbj@uefiknut work]$ DOCK=/home/jovyan/work [knutjbj@uefiknut work]$ docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle $IMAGE --id $ID Create missing output directory /home/jovyan/work/mindboggle123_output Traceback (most recent call last): File "/opt/conda/bin/mindboggle123", line 125, in os.makedirs(OUT) File "/opt/conda/lib/python3.5/os.py", line 241, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/home/jovyan/work/mindboggle123_output'