KeyError while running Morphologist on command line
Posted: Thu Sep 27, 2018 8:36 am
Hello forum members,
I am trying to run the morphologist pipeline on the command line without the bvproc(with normalizaiton enabled). It has 15 arguments.
This is the command used -
And I get the following error -
I tried to debug this error and found that the arguments are parsed into a python dictionary data structure called kwargs, with the parameter name as key and the path/flag as the value. This dict, kwargs, has all the 15 arguemnts successfully stored in it. It is then passed to the morphologist instance of the process class to be stored as an attribute. When it is passed as an attribute to the morphologist instance, only 14 out of 15 arguments are stored and the "commissure_cooridnates" key-value pair is not stored. This is giving rise to the keyerror when the "commissure_cooridnates" key is queried.
Has anybody experienced this error? Do you know what is the issue causing this error?
Thanks,
Durai
I am trying to run the morphologist pipeline on the command line without the bvproc(with normalizaiton enabled). It has 15 arguments.
This is the command used -
Code: Select all
python -m brainvisa.axon.runprocess morphologist \
t1mri=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/220071_1-t1.nii \
perform_normalization=1 \
anterior_commissure=none \
posterior_commissure=none \
interhemispheric_point=none \
left_hemisphere_point=none \
t1mri_nobias=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/nobias_220071_1-t1.nii \
histo_analysis=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/nobias_220071_1-t1.han \
split_brain=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/segmentation/voronoi_220071_1-t1.nii \
left_graph=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/folds/3.1/L220071_1-t1.arg \
right_graph=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/folds/3.1/R220071_1-t1.arg \
perform_sulci_recognition=true \
left_labelled_graph=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/L220071_1-t1_default_session_auto.arg \
right_labelled_graph=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/R220071_1-t1_default_session_auto.arg \
commissure_coordinates=/mnt2/1000BRAINS/subjects/220071_1-t1/t1mri/default_acquisition/220071_1-t1.APC
Code: Select all
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
Headless Anatomist running in normal (non-headless) mode
Traceback (most recent call last):
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/pdb.py", line 1314, in main
pdb._runscript(mainpyfile)
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/pdb.py", line 1233, in _runscript
self.run(statement)
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/bdb.py", line 400, in run
exec cmd in globals, locals
File "<string>", line 1, in <module>
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 404, in <module>
process = get_process_with_params(process_name, iterated, *args, **kwargs)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 131, in get_process_with_params
context._setArguments(*(process,) + tuple(args), **kwargs)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2848, in _setArguments
proc.setValue(argname, v)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 918, in setValue
newValue = self.signature[name].findValue(value)
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/UserDict.py", line 40, in __getitem__
raise KeyError(key)
KeyError: 'commissure_coordinates'
Has anybody experienced this error? Do you know what is the issue causing this error?
Thanks,
Durai