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  • ndcn0236/fsl-pipe-example
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#!/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
...@@ -118,7 +118,7 @@ def run_topup( ...@@ -118,7 +118,7 @@ def run_topup(
outfile: Out("fieldmap/fieldcoef"), outfile: Out("fieldmap/fieldcoef"),
unwarped_b0: Out, 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 # Let's have some simple recipes again
......