Commit 37eb1370 authored by Fidel Alfaro Almagro's avatar Fidel Alfaro Almagro
Browse files

Update bb_pipeline_struct_queue.py

parent 05b9254a
......@@ -44,8 +44,8 @@ def bb_pipeline_struct(subject, runTopup, fileConfiguration, queue, coeff):
else:
numVols=int(sum(bvals<=b0_threshold))
if not os.path.isdir(subject + '/fieldmap/):
os.makedirs(subject + '/fieldmap/)
if not os.path.isdir(subject + '/fieldmap/'):
os.makedirs(subject + '/fieldmap/')
jobGETB01 = LT.runCommand(logger, '${FSLDIR}/bin/fsl_sub -q ' + short_queues + ' -N "bb_get_b0s_1_' + subject + '" -l ' + logDir + ' $BB_BIN_DIR/bb_structural_pipeline/bb_get_b0s.py -i ' + subject + '/dMRI/raw/' + encDir + '.nii.gz -o ' + subject + '/fieldmap/total_B0_' + encDir + '.nii.gz -n ' + str(numVols) + ' -l ' + str(b0_threshold) )
jobsB0.append(LT.runCommand(logger, '${FSLDIR}/bin/fsl_sub -q ' + long_queues + ' -N "bb_choose_bestB0_1_' + subject + '" -l ' + logDir + ' -j ' + jobGETB01 + ' $BB_BIN_DIR/bb_structural_pipeline/bb_choose_bestB0 ' + subject + '/fieldmap/total_B0_' + encDir + '.nii.gz ' + subject + '/fieldmap/B0_' + encDir + '.nii.gz '))
......
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