FATAL: "lit-inpainting": executable file not found in $PATH

[amirhusseinab]

Hi,

I've git cloned the toolbox today, however, while running it using this script:

./neurolit/scripts/run_lit_containerized.sh --singularity \
--input_image ${INPUT_IMG} --mask_image ${seg_file_bin} \
--output_directory ${OUTPUT_DIR} --dilate 2

results in this error:

WARNING: Could not find any nv files on this host!
FATAL:   "lit-inpainting": executable file not found in $PATH

I'm running it on an HPC node without a GPU (hence that nv warning) with Singularity (Docker not installed). Looking forward to your comments.

Best,
Amir

[ClePol]

Hi Amir,

Thanks for your interest.
You cloned the current dev version of the repo, which is currently not compatible with the Docker image online, as we are in the process of releasing the next version.

For now I updated the README to point to the latest (pre-)release:

git clone --filter=blob:none --no-checkout https://github.com/Deep-MI/neurolit.git && \
(cd neurolit && git checkout fda601568d86fce0d07b593215ffd07b45c6b96d) # checkout 0.5.0 release
./neurolit/run_lit_containerized.sh --input_image T1w.nii.gz --mask_image lesion_mask.nii.gz --output_directory output_directory --singularity

This should solve the immediate problem, although I'm currently not able to test it since I'm traveling.

Unfortunately though, we currently do not support running on CPU only as processing can take extremely long (depending on your dataset size of course). Is there any way you can run this on a machine with NVIDIA GPU support?

Best
Clemens