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fix: preserve original datatype on output instead of hardcoding signed short #7

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Merged
akhanf merged 1 commit into from
Jul 9, 2026
Merged

fix: preserve original datatype on output instead of hardcoding signed short #7

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21 changes: 16 additions & 5 deletions run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -364,15 +364,26 @@ do
cp -v $out_nointcorr $out_unwarped
fi

echo "settings datatype to short and resetting header from original image"

#ensure final unwarped (out_unwarped) is same datatype and geom as input (assuming mr images are input type short)
echo fslmaths $out_unwarped $out_unwarped -odt short
fslmaths $out_unwarped $out_unwarped -odt short
echo "settings datatype to match input and resetting header from original image"

#ensure final unwarped (out_unwarped) is same datatype and geom as input
#detect the original datatype so we correctly handle both signed (INT16) and unsigned (UINT16) short
orig_dtype=$(fslinfo $nii | grep "^data_type" | awk '{print $2}')
case "$orig_dtype" in
UINT8) odt="char" ;;
INT16) odt="short" ;;
UINT16) odt="int" ;; # fslmaths has no ushort; INT32 holds all UINT16 values without sign corruption
INT32) odt="int" ;;
FLOAT32) odt="float" ;;
FLOAT64) odt="double" ;;
*) odt="short" ;;
esac
echo fslmaths $out_unwarped $out_unwarped -odt $odt
fslmaths $out_unwarped $out_unwarped -odt $odt
echo fslcpgeom $nii $out_unwarped
fslcpgeom $nii $out_unwarped


#copy extra files
for ext in json bvec bval tsv
do
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