The superres-mri's discuss from brainhack-ch

bids is not in environment.yml

Trying to run the notebook, bids is not installed. It should be required in environment.yml

Silent failure of nipype with Docker

When running a SINAPPS using Docker, the script reports no error but fails to run the executable inside docker if:

docker engine is not running
the relevant Docker image is not present

This should be detected as an error.

Implementation of SINAPPS

List of SINAPPS to be implemented:

Tasks involved for each SINAPP:

Check if interfaces already implemented by Priscille and Hamza
Adapt to sinapp framework or implement interface for each program of the Containerized MIALSRTK library listed above.
Creation of each sinapp underlies the creation of the following files stored under sinapps/<sinapp-name>/ (see sinapps/nlmdenoise/ for an example):
- The implementation of the run.py script which provides a BIDS app argument parser, the creation of the workflow and the execution of the sinapp.
- The implementation of the Dockerfile for containerization that describes the computing environment used to execute the workflow based on an Ubuntu 16.04 LTS system. A conda environment.yml is used to facilitate the installation of the python environment.

Continuous Integration Testing and Delivery

graphviz is missing in the environment.yml

Graphviz should be added to environment.yml, Nipype depends on it to write the execution graph.

Error: BIDSDataGrabber with pybids >= 0.9

BIDS data grabber does not work with pybids >= 0.9:

Jupyter Notebook error:

191108-16:17:18,426 nipype.workflow INFO:
	 Workflow bids_demo settings: ['check', 'execution', 'logging', 'monitoring']
191108-16:17:18,441 nipype.workflow INFO:
	 Running serially.
191108-16:17:18,446 nipype.workflow INFO:
	 [Node] Setting-up "bids_demo.bids_grabber" in "/home/brainhacker/data/derivatives/mialsrtk/bids_demo/bids_grabber".
191108-16:17:18,450 nipype.workflow INFO:
	 [Node] Running "bids_grabber" ("nipype.interfaces.io.BIDSDataGrabber")
191108-16:17:18,899 nipype.workflow WARNING:
	 Storing result file without outputs
191108-16:17:18,901 nipype.workflow WARNING:
	 [Node] Error on "bids_demo.bids_grabber" (/home/brainhacker/data/derivatives/mialsrtk/bids_demo/bids_grabber)
191108-16:17:18,903 nipype.workflow ERROR:
	 Node bids_grabber failed to run on host bh-p05-03.
191108-16:17:18,903 nipype.workflow ERROR:
	 Saving crash info to /home/brainhacker/superres-mri/notebooks/crash-20191108-161718-brainhacker-bids_grabber-2e444a58-15b6-4bc4-b0c8-a98a3b1476bb.pklz
Traceback (most recent call last):
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
    node.run(updatehash=updatehash)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
    result = self._run_interface(execute=True)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 569, in _run_interface
    return self._run_command(execute)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 662, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 384, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/interfaces/io.py", line 2836, in _list_outputs
    derivatives=self.inputs.index_derivatives)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/bids/layout/layout.py", line 226, in __init__
    index_metadata=index_metadata)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/bids/layout/layout.py", line 556, in add_derivatives
    self.derivatives[pipeline_name] = BIDSLayout(deriv, **kwargs)
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/bids/layout/layout.py", line 211, in __init__
    indexer.index_metadata()
  File "/home/brainhacker/miniconda3/envs/supermri-env/lib/python3.7/site-packages/bids/layout/index.py", line 284, in index_metadata
    file_md.update(pl)
ValueError: dictionary update sequence element #0 has length 4; 2 is required

191108-16:17:18,905 nipype.workflow INFO:
	 ***********************************
191108-16:17:18,905 nipype.workflow ERROR:
	 could not run node: bids_demo.bids_grabber
191108-16:17:18,906 nipype.workflow INFO:
	 crashfile: /home/brainhacker/superres-mri/notebooks/crash-20191108-161718-brainhacker-bids_grabber-2e444a58-15b6-4bc4-b0c8-a98a3b1476bb.pklz
191108-16:17:18,907 nipype.workflow INFO:
	 ***********************************
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-6-288982abd1f9> in <module>
     68 
     69 wf.connect(preparePaths, "docker_T2ws_paths", nlmDenoise, "input_images")
---> 70 res = wf.run()

~/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py in run(self, plugin, plugin_args, updatehash)
    597         if str2bool(self.config['execution']['create_report']):
    598             self._write_report_info(self.base_dir, self.name, execgraph)
--> 599         runner.run(execgraph, updatehash=updatehash, config=self.config)
    600         datestr = datetime.utcnow().strftime('%Y%m%dT%H%M%S')
    601         if str2bool(self.config['execution']['write_provenance']):

~/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py in run(self, graph, config, updatehash)
     69 
     70         os.chdir(old_wd)  # Return wherever we were before
---> 71         report_nodes_not_run(notrun)

~/miniconda3/envs/supermri-env/lib/python3.7/site-packages/nipype/pipeline/plugins/tools.py in report_nodes_not_run(notrun)
     93                 logger.debug(subnode._id)
     94         logger.info("***********************************")
---> 95         raise RuntimeError(('Workflow did not execute cleanly. '
     96                             'Check log for details'))
     97 

RuntimeError: Workflow did not execute cleanly. Check log for details

Docker-out-of-Docker (DooD) Solution

Brainhack Global Geneva 2019 Challenge

Build and run a Docker image executes a nipype workflow that should run an other Docker image that contains the C++ NLMdenoising program of the MIALSRTK library.

Road Map:

Creation of first sinapp workflow with BIDS App parser (python / not containerized yet)
Creation of Dockerfile
Build, test, and make it work

Update README

Running the python notebook does not work
Add instructions for docker container (mial-srtk)

brainhack-ch / superres-mri Goto Github PK

superres-mri's Issues

bids is not in environment.yml

Silent failure of nipype with Docker

Implementation of SINAPPS

Continuous Integration Testing and Delivery

graphviz is missing in the environment.yml

Error: BIDSDataGrabber with pybids >= 0.9

Jupyter Notebook error:

Docker-out-of-Docker (DooD) Solution

Update README

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