failed visualisation of diffusion outputs

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Isotta Rigoni

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Apr 30, 2021, 4:32:27 AMApr 30
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Good morning,
I am writing as I am trying to visualize the output of the diffusion pipeline but I am failing so far.
 
I am using the Connectome Mapper v3.0.0-RC4 with Freesurfer 6.0.1. I have run the anatomical and diffusion pipeline uploaded on Zenodo (with 'dipy_recon_config.mapmri=false) on the ds-sample dataset.
The processing ran smoothly without errors. However, when I try to visualize the outcomes of the PREPROCESSING, REGISTRATION and RECONSTRUCTION+TRACTOGRAPHY steps, I get the following messages: (depending on what outcomes I try to visualise)

Exception occurred in traits notification handler for object: <cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI object at 0x7f432ae55470>, trait: inspect_output_button, old value: <undefined>, new value: 0
Traceback (most recent call last):
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/trait_notifiers.py", line 381, in __call__
    self.handler(*args)
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/stages/connectome/connectome.py", line 167, in _inspect_output_button_fired
    subprocess.Popen(self.inspect_outputs_dict[self.inspect_outputs_enum])
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'trackvis': 'trackvis'




Exception occurred in traits notification handler for object: <cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI object at 0x7f432ae55ef0>, trait: inspect_output_button, old value: <undefined>, new value: 0
Traceback (most recent call last):
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/trait_notifiers.py", line 381, in __call__
    self.handler(*args)
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/stages/preprocessing/preprocessing.py", line 144, in _inspect_output_button_fired
    subprocess.Popen(self.inspect_outputs_dict[self.inspect_outputs_enum])
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "/home/degano/anaconda3/envs/py37cmp-gui/lib/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mrview': 'mrview'


However, with the visualisation of the STRUCTURAL CONNECTOME step, everything goes well.

Do you think it is due to a problem with the installation of the softwares used in the visualisation step? Or might it be due to the fact that some of these outcomes were not directly saved to the derivatives/cmp/.../dwi folder?
Thanks in advance,
Isotta

Sebastien Tourbier

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Apr 30, 2021, 7:49:29 AMApr 30
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Hi Isotta!

The quality inspector is indeed generating the command to open the outputs with appropriate visualization tools. While, fsleyes is already included in the miniconda environment, you will need to install FreeSurfer 6 (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/) to visualize the the parcellation with freeview, mrtrix3 to visualize a number of diffusion pipeline outputs with mrview (conda install -c mrtrix3 mrtrix3=v3.0.2 ; this will be directly included in the conda environment of the next release), and trackvis (http://trackvis.org/download/) to visualize tractograms.

Best,
Sebastien

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