PeerHerholz
commented
2 years ago Hi @MarioXu,
thank you very much for opening this issue.
Could you maybe provide further information re your setup and how you tried to run mindboggle, ie. what OS are you using and what do HOST and DOCK refer to? The error itself suggests that the path inside/outside the container is not correctly specified/mapped.
Cheers, Peer
Dear Sir The error is below when I am running a test, how to fixed it ? Thanks a lot !
sudo docker run --env-file /home/xubin/.env --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID [sudo] password for xubin: INFO: /root/matlab/startup.m does not exist ... creating Running mindboggle version 1.3.8 (latest: 1.3.8) 220803-02:44:13,303 nipype.utils INFO: Running nipype version 1.3.0-rc1 (latest: 1.8.3) Traceback (most recent call last): File "/opt/miniconda-latest/envs/mb/bin/mindboggle123", line 170, in
reconall.inputs.T1_files = IMAGE
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 400, in validate
value = super(MultiObject, self).validate(objekt, name, newvalue)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/traits/trait_types.py", line 2573, in validate
return TraitListObject(self, object, name, value)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/traits/trait_handlers.py", line 2474, in init
raise excp
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/traits/trait_handlers.py", line 2466, in init
value = [validate(object, name, val) for val in value]
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/traits/trait_handlers.py", line 2466, in
value = [validate(object, name, val) for val in value]
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 317, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 141, in validate
self.error(objekt, name, str(value))
File "/opt/miniconda-latest/envs/mb/lib/python3.6/site-packages/traits/trait_handlers.py", line 236, in error
object, name, self.full_info(object, name, value), value
traits.trait_errors.TraitError: Each element of the 'T1_files' trait of a ReconAllInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/jovyan/work/example_mri_data/T1.nii.gz' <class 'str'> was specified.