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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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How to Specify the data directory? #101

Closed BrianYahoo closed 11 months ago

BrianYahoo commented 1 year ago

When I want to specify the bids directory as "./bids", and I'm sure this "./bids/sub-01/ses-01" does exist

In the terminal line, I wrote "docker run -ti --rm micalab/micapipe:v0.2.2 -bids ./bids -out ./prop -sub 01 -ses 01 -proc_structural".

Then it actually runs "micapipe -bids ./bids -out ./prop -sub 01 -ses 01 -proc_structural", which is correct.

However, the OUTPUT is completely confusing because it reports

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

Why is micapipe doing at this "/home/mica/bids" directory? I don't know how to specify the working directory to a local path, could anyone help me? Because this pipeline seems really powerful so I really want to learn how to use it!

BrianYahoo commented 1 year ago

When I tried input the absolute path of a directory as below: "micapipe -bids /data/bryang/human/WenZ/fMRI/bids -out /data/bryang/human/WenZ/fMRI/prop -sub 01 -ses 01 -proc_structural"

The OUTPUT is still confusing because these two directory do exist: realpath: /data/bryang/human/WenZ/fMRI/prop: No such file or directory realpath: /data/bryang/human/WenZ/fMRI/bids: No such file or directory and [ ERROR ]..... 01 was not found on the BIDS directory Check ls /sub-01/ses-01

Therefore I'm done, that's as far as I can go.

rcruces commented 11 months ago

This issue is related to the issue #100, I will close this and continue there. It is highly likely that by mounting correctly the directories with -v will fix it.