code/preprocessing.py at main · valentinelahy/code · GitHub

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import elikopy
import sys
import json
from pathlib import Path

modulename = 'elikopy'
if modulename not in sys.modules:
    print('You have not imported the module')

# f_path = "/auto/home/users/v/l/vlahy/dataset/"
root_in  = "/CECI/proj/pilab/PermeableAccess/alzheimer_kDs4Eb69VO/study/"
root_out = "/globalscratch/ucl/elen/vlahy/tractogram/"
json_file = Path(root_in) / "subjects" / "subj_list.json"

subjects = json.loads(json_file.read_text())
subjects_10 = subjects[:10] # take the first 10 subjects for testing

study = elikopy.core.Elikopy(root_in, slurm=True, slurm_email='valentine.lahy@student.uclouvain.be',cuda=False)
# patient_list=study.patient_list(f_path)

# Alzheimer
# study.preproc(
#   eddy=True,
#   denoising=True,
#    reslice=True,
#   gibbs=False,
#   topup=True,
#    forceSynb0DisCo=True,
#    patient_list_m=patient_list,
#    cpus=2,
#    slurm_timeout="24:00:00")
# study.odf_msmtcsd(patient_list_m=patient_list,slurm_timeout="00:45:00")
study.tracking(folder_path=root_in,save_as_trk=True, output_dir=root_out, streamline_number=500000,patient_list_m=subjects_10, slurm_timeout="06:00:00")

# study.dti(patient_list_m=patient_list)
# study.noddi(patient_list_m=patient_list,slurm_timeout="20:00:00")