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License: BSD 3-Clause "New" or "Revised" License
Add the 526 model into BIBSnet and CABINET,
Hi!
I want to pull the singularity image, but pulling is not finished successfully.
I would appreciate your help,
Parinaz.
singularity pull docker://dcanumn/bibsnet
main
parinazbabaeeghazvini@Parinazs-MacBook-Pro ~ % singularity pull docker://dcanumn/bibsnet
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO: Starting build...
Getting image source signatures
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Writing manifest to image destination
Storing signatures
FATAL: Unable to pull docker://dcanumn/bibsnet: packer failed to pack: While unpacking tmpfs: unpack: error extracting layer: link /var/folders/dy/9095hyps7nd4pqh6_jjldt1h0000gn/T/sbuild-385127066/fs/opt/conda/pkgs/ncurses-6.2-h58526e2_4/share/terminfo/N/NCR260VT300WPP /var/folders/dy/9095hyps7nd4pqh6_jjldt1h0000gn/T/sbuild-385127066/fs/opt/conda/share/terminfo/N/NCR260VT300WPP: too many levels of symbolic links
No response
Looks like NVIDIA maintains a version of nnUNet along with optimizations to it based on subsequent GPU releases. We should definitely use this, it even contains a Dockerfile! https://github.com/NVIDIA/DeepLearningExamples/tree/master/PyTorch/Segmentation/nnUNet
BIBSNet has this strange requirement where it wants to write a JSON file (postprocessing.json) into the container. The upside is that this does not prevent the segmentations from being created, however, I'm afraid that it could cause the pipeline to terminate if it is run non-interactively.
Traceback (most recent call last): File "/opt/conda/bin/nnUNet_predict", line 33, in <module> sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_predict')()) File "/home/nnUNet/nnunet/inference/predict_simple.py", line 217, in main predict_from_folder(model_folder_name, input_folder, output_folder, folds, save_npz, num_threads_preprocessing, File "/home/nnUNet/nnunet/inference/predict.py", line 658, in predict_from_folder return predict_cases(model, list_of_lists[part_id::num_parts], output_files[part_id::num_parts], folds, File "/home/nnUNet/nnunet/inference/predict.py", line 277, in predict_cases shutil.copy(pp_file, os.path.abspath(os.path.dirname(output_filenames[0]))) File "/opt/conda/lib/python3.8/shutil.py", line 418, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/opt/conda/lib/python3.8/shutil.py", line 264, in copyfile with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst: PermissionError: [Errno 13] Permission denied: '/opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet/3d_fullres/Task512_BCP_ABCD_Neonates_SynthSegDownsample/nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json' Traceback (most recent call last): File "/home/bibsnet/run.py", line 178, in <module> main() File "/home/bibsnet/run.py", line 25, in main run_nnUNet_predict(cli_args) File "/home/bibsnet/run.py", line 39, in run_nnUNet_predict subprocess.check_call((cli_args["nnUNet"], File "/opt/conda/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '('/opt/conda/bin/nnUNet_predict', '-i', '/input', '-o', '/output', '-t', '512', '-m', '3d_fullres')' returned non-zero exit status 1.
https://3.basecamp.com/5032058/buckets/21517584/todolists/6232959206
No :(
Hi!
I want to segment T1w and T2w images of an infant using BIBSnet. I already followed the instruction for naming the files. I downloaded the package, and I used the following command:
python3 run.py --input /Users/p/Desktop/data --output /Users/p/Desktop/data/seg --task 512 --nnUNet ? --model 3d_fullres
Here is the error message:
run.py: error: argument --nnUNet/-n: Cannot read file at '/Users/p/Documents/BIBSnet/nnUNet_predict'
But I don't know where I can find "nnUNet_predict".
I have already downloaded the "3d_fullres" package, and I fetched the "nnUNet" from the GuitHub using the following code:
git clone https://github.com/MIC-DKFZ/nnUNet.git
cd nnUNet
pip install -e .
but it didn't solve the problem.
Would you please help me to solve this issue?
Thank you in advance,
Parinaz.
python3 run.py --input /Users/p/Desktop/data --output /Users/p/Desktop/data/seg --task 512 --nnUNet ? --model 3d_fullres
main
run.py: error: argument --nnUNet/-n: Cannot read file at '/Users/p/Documents/BIBSnet/nnUNet_predict'
I have already downloaded the "3d_fullres" package, and I fetched the "nnUNet" from the GuitHub using the following code:
git clone https://github.com/MIC-DKFZ/nnUNet.git
cd nnUNet
pip install -e .
But it didn't solve the problem.
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