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NeuroDesk / neurocontainers

The containers can be used in combination with our transparent singularity or neurocommand tool, that wrap the executables inside a container to make them easily available for pipelines
https://www.neurodesk.org
MIT License
21 stars 53 forks source link

add HCP pipelines #63

Open stebo85 opened 3 years ago

stebo85 commented 3 years ago

https://github.com/Washington-University/HCPpipelines

lucsanara commented 1 month ago

Hi!! was this already implemented?

stebo85 commented 1 month ago

Yes, we have a bidsapp for these pipelines: bidsapphcppipelines_4.3.0

lucsanara commented 1 month ago

I am trying to work with hcpasl pipeline but do not succeed. Should it be also installed? https://github.com/physimals/hcp-asl

stebo85 commented 1 month ago

Dear @lucsanara - the hcp-asl pipeline is not yet available in Neurodesk, but I opened an issue for it now: https://github.com/NeuroDesk/neurocontainers/issues/765 . Do you want to try to contribute this pipeline to Neurodesk?

lucsanara commented 1 month ago

Sure! Not sure how it works to install it. I ran: conda create -n hcpasl python=3.11 cython 'numpy>=1.25' conda activate hcpasl pip install git+https://github.com/physimals/hcp-asl.git It did not work when entering the command process_hcp_asl

stebo85 commented 1 month ago

@lucsanara - it needs a few more things to make this work. We can try to have a look at this in the next weeks - would that work for you or do you need it urgently?