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DevelopmentalImagingMCRI / karawun

Convert tractography studies from mrtrix into dicom for use in navigation software
Apache License 2.0
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empty label file #2

Closed LucSam closed 4 years ago

LucSam commented 4 years ago

Hi, when we export labels, such as a ROI, we get an empty file, it's not visible in Brainlab. The crosshairs however indicate the right position though. The ROI is based on a T1 which has been provided as a nii file to the command. It works fine for the tracts. Do you have a suggestion how to overcome that problem?

Best, Lucius

importTractography --dicom-template path/to/dicom/slice.dcm --nifti t1.nii.gz fa.nii.gz ROI.nii.gz --tract-files tract.tck --label-files ROI.nii.gz -o .

richardbeare commented 4 years ago

Thanks for the test - can you send the samples for debugging?

A couple of thoughts. I have noticed that some label files, with lots of different labels, can take a while for brainlab to convert. The other possibility is that the label value is too high - currently it only supports values up to 30.

Also, I haven't tested using the same image in both the --nifti and the --label-files option. If ROI.nii.gz is derived from t1.nii.gz, then the following is meant to work:

importTractography --dicom-template path/to/dicom/slice.dcm --nifti t1.nii.gz fa.nii.gz  --tract-files tract.tck --label-files ROI.nii.gz -o ./Patient/
LucSam commented 4 years ago

Thank you very much, we detected the issue which occurred by a brainlab employee by anonymising the data.

richardbeare commented 4 years ago

Confirming - you see what you expect to see in brainlab? If so I will create an official release for this point.

LucSam commented 4 years ago

Confirming - you see what you expect to see in brainlab? If so I will create an official release for this point.

Yes, I can confirm that it works

richardbeare commented 4 years ago

Thanks. I will tag the release tomorrow.