[general need] FSL is no longer working in mia

[servoz]

It is not known since how long. First investigation indicate that with all populse on master:

• capsul at 618f3fa0 commit and populse_mia at aeb88cb4 commit => it's working
• capsul at 618f3fa0 commit and populse_mia at d640d339 => it's not working exception:

  
  File "<string>", line 1, in <module>
  File "/casa/host/src/capsul/master/capsul/process/process.py", line 731, in run_from_commandline
  result = ce.study_config.run(process, configuration_dict=configuration)
  File "/casa/host/src/capsul/master/capsul/study_config/study_config.py", line 429, in run
  configuration_dict=configuration_dict)
  File "/casa/host/src/capsul/master/capsul/study_config/run.py", line 165, in run_process
  returncode = process_instance._run_process()
  File "/casa/home/Git_projects/populse_mia/python/populse_mia/user_interface/pipeline_manager/process_mia.py", line 518, in _run_process
  self.run_process_mia()
  File "/casa/home/Git_projects/mia_processes/python/mia_processes/bricks/preprocess/fsl/processes.py", line 230, in run_process_mia
  return self.process.run(configuration_dict={})
  File "/casa/host/src/capsul/master/capsul/process/process.py", line 310, in run
  return self.__call__(**kwargs)
  File "/casa/host/src/capsul/master/capsul/process/process.py", line 302, in __call__
  returncode = self.get_study_config().run(self, **kwargs)
  File "/casa/host/src/capsul/master/capsul/study_config/study_config.py", line 429, in run
  configuration_dict=configuration_dict)
  File "/casa/host/src/capsul/master/capsul/study_config/run.py", line 165, in run_process
  returncode = process_instance._run_process()
  File "/casa/host/src/capsul/master/capsul/process/process.py", line 1877, in _run_process
  results = self._nipype_interface.run()
  File "/casa/home/.local/lib/python3.6/site-packages/nipype-1.7.1-py3.6.egg/nipype/interfaces/base/core.py", line 398, in run
  runtime = self._run_interface(runtime)
  File "/casa/home/.local/lib/python3.6/site-packages/nipype-1.7.1-py3.6.egg/nipype/interfaces/base/core.py", line 756, in _run_interface
  % (executable_name, runtime.hostname)
  OSError: No command "fslmaths" found on host irmage-rico. Please check that the corresponding package is installed.

Same result using nipype 1.7.0 (not tested before)

Quick and dirty solution while waiting for a fix:
Add in .bashrc:

FSLDIR= . ${FSLDIR}/etc/fslconf/fsl.sh PATH=${FSLDIR}/bin:${PATH} export FSLDIR PATH

[LStruber]

In software_properties.py, if I change line 392: m['directory'] = os.path.dirname(fsl_config) by: m['directory'] = os.path.dirname('/home/lucas/apps/fsl/bin')

It works. Of course it should be done cleanly (by removing 'fslconf' at the end of fsl_config directory and adding 'bin'). But as you are the one that works a lot on synchronization between Capsul config and MIA preferences, you may potential implication/alter effects that I don't see. Any ideas ?

[LStruber]

by removing 'fslconf' at the end of fsl_config directory and adding 'bin'

Adding bin is not necessary. The following lines are working:

m['directory'] = os.path.split(
                os.path.split(
                    os.path.dirname(fsl_config))[0])[0]

I'm waiting for your opinion before pushing

[servoz]

Oh great !! You found the issue exactly !!!

It looks like a (big) typo :-).

I would prefer to replace l392 m['directory'] = os.path.dirname(fsl_config) with

m['directory'] = os.path.dirname(
                                 os.path.dirname(
                                     os.path.dirname(fsl_config)))

but indeed

m['directory'] = os.path.split(
                os.path.split(
                    os.path.dirname(fsl_config))[0])[0]

do also the job !

I will leave to you the pleasure to push the change and close this ticket. Cool!

[LStruber]

closed with 73f121707d25b3f2ee3d28cb57981313cd6ea6cd