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Check if required inputs exist in pipeline.sh #8

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15 changes: 15 additions & 0 deletions src/pipeline.sh
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,21 @@ export PATH=$PATH:$ANTSPATH:/extra/ANTS/ANTs/Scripts
# Set up pytorch
source /extra/pytorch/bin/activate

# Check input
if [[ ! -f /INPUTS/b0.nii.gz ]]; then
echo ERROR: Could not find required input /INPUTS/b0.nii.gz
exit
elif [[ ! -f /INPUTS/T1.nii.gz ]]; then
echo ERROR: Could not find required input /INPUTS/T1.nii.gz
exit
elif [[ ! -f /INPUTS/acqparams.txt ]]; then
echo ERROR: Could not find required input /INPUTS/acqparams.txt
exit
elif [[ ! -f /extra/freesurfer/license.txt ]]; then
echo ERROR: Could not find required /extra/freesurfer/license.txt
exit
fi

# Prepare input
prepare_input.sh /INPUTS/b0.nii.gz /INPUTS/T1.nii.gz /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c.nii.gz /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz /OUTPUTS

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