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MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
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Ran commands successfully but no results files generated #31

Closed jhx9327 closed 1 year ago

jhx9327 commented 2 years ago

Hi!

I ran micapipe by docker with the following commands: docker run -ti --rm \ -v /my_path/bids:/data:ro \ -v /my_patht/micapipe/derivatives:/out \ -v /my_path/micapipe/working_directory:/tmp \ -v /my_path/license.txt:/opt/freesurfer/license.txt \ micalab/micapipe:latest -bids /data -out /out \ -proc_structural -sub 03 04 -threads 10 -tracts 10M

It seems that it ran successfully but there is no results generated under derivative and working_dirctory except these. The folders of freesurfer and sub-03 can not be opened or deleted. My input data is in BIDS format which can be used to fmriprep (so I guess it might not result from my data). micapipe ├── derivatives │   ├── freesurfer [error opening dir] │   └── micapipe │   ├── micapipe_processed_sub.csv │   ├── pipeline-description.json │   └── sub-03 [error opening dir] └── working_directory

Thank you so much if you can give me any idea to deal with this. Happy holiday!

rcruces commented 1 year ago

I believe that this is a permission issue, and if you have problems creating the container it's better for you to contact your administrator. Here is more information regarding the container generation: documentation