gen_input_data.sh

+#!/usr/bin/env sh
+
+mkdir input
+for subject in 100307 103818 ; do
+    directory=input/${subject}/unprocessed/3T/Diffusion
+    mkdir -p ${directory}
+    for dir in 95 96 97 ; do
+        for pe in LR RL ; do
+            touch ${directory}/${subject}_3T_DWI_dir${dir}_${pe}.nii.gz
+            touch ${directory}/${subject}_3T_DWI_dir${dir}_${pe}.bval
+            touch ${directory}/${subject}_3T_DWI_dir${dir}_${pe}.bvec
+        done
+    done
+done

pipe.py

@@ -118,7 +118,7 @@ def run_topup(
         outfile: Out("fieldmap/fieldcoef"),
         unwarped_b0: Out,
         ):
-    topup(merged_b0s, acqparams, out=topup_basename, iout=unwarped_b0)
+    topup(merged_b0s, acqparams, out=topup_basename, iout=unwarped_b0, config="b02b0_1.cnf")
 
 
 # Let's have some simple recipes again