gift-surg / monaifbs Goto Github PK
View Code? Open in Web Editor NEWLicense: Apache License 2.0
License: Apache License 2.0
Hello,
I'm trying to rebuild a new singularity container embeding MONAIfbs but.
no matter the way I try to get the models archive it fails.
+ zenodo_get 10.5281/zenodo.4282679
Title: MONAI dynUNet model for fetal brain segmentation
Keywords: fetal brain segmentation, MONAI, dynUNet
Publication date: 2020-11-20
DOI: 10.5281/zenodo.4282679
Total size: 324.5 MB
Link: https://zenodo.org/api/files/ba541695-648a-4f20-9995-ee86cb1ccb6a/models.tar.gz size: 324.5 MB
Download error. Original link: https://zenodo.org/api/files/ba541695-648a-4f20-9995-ee86cb1ccb6a/models.tar.gz
Too many errors.
Download is aborted.
wget https://zenodo.org/api/files/ba541695-648a-4f20-9995-ee86cb1ccb6a/models.tar.gz
also fail
is there another way or URL source to get the archive ?
Eric
Dear .
I gave a try to the docker version of the great fetal brain segmentation tool you provide. I ran the fetal brain segmentation of 3 stacks using niftymic segmentation command. I should precise I ran the docker with singularity on a high performance computing cluster (slurm interface). When launching the segmentation I obtained the error below:
File "fetal_brain_seg.py", line 86, in
run_inference(input_data=img, config_info=config)
File "/app/NiftyMIC/MONAIfbs/monaifbs/src/inference/monai_dynunet_inference.py", line 273, in run_inference
evaluator.run()
File "/usr/local/lib/python3.6/site-packages/monai/engines/evaluator.py", line 91, in run
super().run()
File "/usr/local/lib/python3.6/site-packages/monai/engines/workflow.py", line 157, in run
super().run(data=self.data_loader, max_epochs=self.state.max_epochs)
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 691, in run
return self._internal_run()
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 762, in _internal_run
self._handle_exception(e)
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 465, in _handle_exception
self._fire_event(Events.EXCEPTION_RAISED, e)
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 423, in _fire_event
func(*first, *(event_args + others), **kwargs)
File "/usr/local/lib/python3.6/site-packages/monai/handlers/stats_handler.py", line 145, in exception_raised
raise e
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 722, in _internal_run
self._fire_event(Events.STARTED)
File "/usr/local/lib/python3.6/site-packages/ignite/engine/engine.py", line 423, in _fire_event
func(*first, *(event_args + others), **kwargs)
File "/usr/local/lib/python3.6/site-packages/monai/handlers/checkpoint_loader.py", line 82, in call
checkpoint = torch.load(self.load_path, map_location=self.map_location)
File "/usr/local/lib/python3.6/site-packages/torch/serialization.py", line 525, in load
with _open_file_like(f, 'rb') as opened_file:
File "/usr/local/lib/python3.6/site-packages/torch/serialization.py", line 212, in _open_file_like
return _open_file(name_or_buffer, mode)
File "/usr/local/lib/python3.6/site-packages/torch/serialization.py", line 193, in init
super(_open_file, self).init(open(name, mode))
PermissionError: [Errno 13] Permission denied: '/app/NiftyMIC/MONAIfbs/monaifbs/models/checkpoint_dynUnet_DiceXent.pt'
The .pt file seems to exist (at least when I run the singularity image) but the script serialization.py can not read it.
Do you have any hint ?
Have a good day
Alex
Hello! I saw a typo in requirements.txt: the last sentence ends with a colon: tensorboard>=2.2.1:
, where it shouldn't.
This thows an error when trying to install it using pip install -e .
Cheers!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.