running error

[MarioXu]

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.

[PeerHerholz]

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