It basically does this at the moment:
- Iterate the patient samples and each patient visit.
- Where it looks like something is incomplete, complete that part of the workflow above, otherwise skip – I know my tests for readiness are incomplete here
- Take some measurements once completed
Running Tests:
Create a folder Patients and fill with samples 0001, 0002
python atlas.py ~/Documents/Patients
#Virtual Environment
python3 -m venv ~/projects/environmens/crush
source ~/projects/environments/crush/bin/activate
#Executions ./crush -samples /media/dmattie/GENERAL/CRUSHDATA -status ./crush -samples /media/dmattie/GENERAL/CRUSHDATA
#Issues with old python 3 libss try: sudo pip3 install -U nibabel
#libgsl.so.0
whereis libgsl.so.0 GSL is provided by the "gsl" module. However in your case you have a precompiled application. You'd either need to compile it from source or try this which would be easier:
module load gsl/1.16 setrpaths.sh --path ~/projects/def-jlevman/dmattie/bin/dtk --add_path=$EBROOTGSL/lib
this modifies the binaries in that folder to look in $EBROOTGSL/lib which contains libgsl.so.0.
#GLobus ./globusconnect -start
55167189
find . -name *.json -print > ~/allgjson.txt
tar -cvf allgjson.tar -T ~/allgjson.txt
find . -name *.out -print | tar -zcvf outs.tar.gz -T
find /scratch/dmattie/crushdata -name *.json -print | xargs tar -czvf ~/projects/dmattie/json.tar.gz
sed -i -e 's/^/levman//' tracts.txt find . -name 'tracts.txt' -exec sed -i 's/^/levman//' {} +