Update bb_pipeline_struct_queue.py with check of fieldmap directory

bb_structural_pipeline/bb_pipeline_struct_queue.py

@@ -43,8 +43,9 @@ def bb_pipeline_struct(subject, runTopup, fileConfiguration, queue, coeff):
                     numVols = 1
                 else:
                     numVols=int(sum(bvals<=b0_threshold))
-                
-       
+
+                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 '))