Open
Milestone
The setup for the CAT processing of UKbiobank
Milestone ID: 334
The container should be modified such that essentially /code/cat_standalone.sh
becomes the runscript
(or rather a thing wrapper around it). It would need to be able to accept any batch file at any location (given appropriate bind mounts).
The setup we would use for internal processing is this. For CAT preprocessing of the UKbiobank we:
- create a fresh datalad dataset to receive the outputs
- we attach the CAT singularity container to it
- we add an appropriate (customized) batch file to the dataset
- we add Juergen's code that extracts the wanted pieces from the CAT output
- we compose a script that, for a single participant, calls the container on the right image file, then calls Jürgens code to move the desired pieces into the final locations, deletes everything else
- let condor process all subjects.
All issues for this milestone are closed. You may close this milestone now.