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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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ReadTheDocs Singularity issues/errors #53

Closed thomshaw92 closed 1 year ago

thomshaw92 commented 1 year ago

Currently: singularity run --cleanenv /my_images/micapipe-.simg \ -B path/to/your/bids_dataset:/bids_dataset:ro \ -B path/to/your/bids_dataset/derivatives:/output_directory \ -B path/to/your/working_directory:/tmp \ -B path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/freesurfer_license_file.txt \ micapipe.simg \ -bids /bids_dataset \ -out /output_directory \ -all -ses 01 \ -threads 10 -tracts 10M

Should be changed to: singularity run --cleanenv \ -B path/to/your/bids_dataset:/bids_dataset:ro \ -B path/to/your/bids_dataset/derivatives:/output_directory \ -B path/to/your/working_directory:/tmp \ -B path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \ /path/to/container/micapipe.simg \ -bids /bids_dataset \ -out /output_directory \ -all -ses 01 \ -threads 10 -tracts 10M :)

rcruces commented 1 year ago

Thanks for this comment, we fixed with the acceptance of the paper!! https://micapipe.readthedocs.io/en/latest/pages/01.install/index.html