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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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realpath No such file or directory #100

Closed BrianYahoo closed 8 months ago

BrianYahoo commented 1 year ago

I tried to use micapipe as follows:

docker run -ti --rm \ micalab/micapipe:v0.2.2 \ -bids '../fMRI/bids' \ -out '../fMRI/prop' \ -fs_licence '../../license.txt' \ -sub 01 \ -proc_structural \ -proc_surf \ -post_structural \ -proc_func

but I get these errors:

realpath: ../fMRI/prop: No such file or directory realpath: ../fMRI/bids: No such file or directory

[ ERROR ]..... 01 was not found on the BIDS directory Check ls /sub-01

But actually this directory does exist, I don't know how to fix this bug. What's wrong with my code?

rcruces commented 11 months ago

Hi, in order to run the docker container your directories must have other read and write permissions and they must me mounted on the container with -v. See the documentation for an example:

https://micapipe.readthedocs.io/en/latest/pages/01.install/index.html