Testing inference on whole volume

[jcohenadad]

Copy 3D volume to folder:

mkdir data_test
cp ${PATH_DATA}/sub-01/anat/sub-01_part-mag_chunk-02_T2starw.nii.gz data_test
cd data_test

Need to split it:

sct_image -i sub-01_part-mag_chunk-02_T2starw.nii.gz -split y 

Then add _0000 as required by nnUNet:

for file in *.nii.gz; do
  base="${file%.nii.gz}"
  mv "$file" "${base}_0000.nii.gz"
done

Run inference:

cd ..
nnUNetv2_predict -i test_set2 -o test_set2_predictions -d 502 -c 2d -f 0 -tr nnUNetTrainerWandb -chk checkpoint_best.pth -device mps

Note

nnUNet stacks it back to a 3D volume 😊