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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
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eddy_openmp --help warning (update dockerhub?) #36

Closed dkp closed 5 years ago

dkp commented 5 years ago

I downloaded from dockerhub. I now see that the last build on dockerhub was a year ago...and probably accounts for this issue. the docker run complains about a call to eddy_openmp --help (see bolding below):

dpat@Saci:/Volumes/Main/Working/DockerMRtrix% docker run -i --name mr3 -v /Volumes/Main/Working/DockerMRtrix:/bids_dataset -v /tmp/derivatives:/outputs bids/mrtrix3_connectome /bids_dataset /outputs participant --participant_label 02 --parcellation desikan
mrtrix3_connectome.py:
mrtrix3_connectome.py: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
mrtrix3_connectome.py:
Command:  bids-validator /bids_dataset
mrtrix3_connectome.py: Commencing execution for subject sub-02
mrtrix3_connectome.py: N4BiasFieldCorrection and ROBEX found; will use for bias field correction and brain extraction
mrtrix3_connectome.py: Generated temporary directory: /mrtrix3_connectome.py-tmp-CN4AJK/
mrtrix3_connectome.py: Importing DWI data into temporary directory
Command:  mrconvert /bids_dataset/sub-02/dwi/sub-02_dwi.nii.gz -fslgrad /bids_dataset/sub-02/dwi/sub-02_dwi.bvec /bids_dataset/sub-02/dwi/sub-02_dwi.bval -json_import /bids_dataset/sub-02/dwi/sub-02_dwi.json /mrtrix3_connectome.py-tmp-CN4AJK/dwi1.mif
mrtrix3_connectome.py: Importing fmap data into temporary directory
mrtrix3_connectome.py: Importing T1 image into temporary directory
Command:  mrconvert /bids_dataset/sub-02/anat/sub-02_T1w.nii.gz /mrtrix3_connectome.py-tmp-CN4AJK/T1.mif
mrtrix3_connectome.py: Changing to temporary directory (/mrtrix3_connectome.py-tmp-CN4AJK/)
mrtrix3_connectome.py: Performing MP-PCA denoising of DWI data
Command:  dwidenoise dwi1.mif dwi1_denoised.mif
mrtrix3_connectome.py: Performing Gibbs ringing removal for DWI data
Command:  mrdegibbs dwi1_denoised.mif dwi1_denoised_degibbs.mif -nshifts 50
mrtrix3_connectome.py: Performing various geometric corrections of DWIs

Command: eddy_openmp --help mrtrix3_connectome.py: [WARNING] Command failed: eddy_openmp --help

Command:  dwipreproc dwi1_denoised_degibbs.mif dwi_preprocessed.mif -rpe_header
Lestropie commented 5 years ago

Hi @dkp,

The issue here is that the FSL command eddy_openmp yields a non-zero return code (typically indicative of an error) when printing its help page. I request the help page of that particular command in order to determine whether or not certain command-line options are available, which is itself necessary in case the Python script mrtrix3_connectome.py is used outside of the container environment (in which case there are no guarantees as to whether or not the user has an up-to-date version of eddy). In turn, the MRtrix3 Python libraries that I'm utilising here yield a warning whenever a command produces a non-zero return code, even if instructed to continue processing despite such an error. Hence the warning you see there.

The only way I can resolve this erroneous warning is via substantial changes to the MRtrix3 Python libraries, which will take some time to get merged into MRtrix3 before I can update this App accordingly.

Rob

dkp commented 5 years ago

thanks very much for the feedback! I won’t worry about it. -Dianne

On Wed, Dec 5, 2018 at 3:32 PM Robert Smith notifications@github.com wrote:

Hi @dkp https://github.com/dkp,

The issue here is that the FSL command eddy_openmp yields a non-zero return code (typically indicative of an error) when printing its help page. I request the help page of that particular command in order to determine whether or not certain command-line options are available https://github.com/BIDS-Apps/MRtrix3_connectome/blob/master/mrtrix3_connectome.py#L364-L372, which is itself necessary in case the Python script mrtrix3_connectome.py is used outside of the container environment (in which case there are no guarantees as to whether or not the user has an up-to-date version of eddy). In turn, the MRtrix3 Python libraries that I'm utilising here yield a warning whenever a command produces a non-zero return code, even if instructed to continue processing despite such an error. Hence the warning you see there.

The only way I can resolve this erroneous warning is via substantial changes to the MRtrix3 Python libraries https://github.com/MRtrix3/mrtrix3/pull/1449, which will take some time to get merged into MRtrix3 before I can update this App accordingly.

Rob

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/36#issuecomment-444677065, or mute the thread https://github.com/notifications/unsubscribe-auth/AA66QP6OaFaPpZJTqq3Ko-T9xVoA3B5oks5u2ElggaJpZM4Y4Ouk .

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