QC of the dataset

[plbenveniste]

Here is the QC of the dataset ran with SCT version git-master-90fb8654fad06eb94fc4d83075b5a1192c22fea4. We look at spinal cord segmentations to inspect the quality of the images.

QC file: sc_seg_qc.zip

I assigned fail when the spinal cord segmentation was not complete, suspecting a problem in the image (artefact, motion,, blur...)
Here is the list of QC fails:

FILES_SEG:
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.5.1762879515.1876.1028546765.349.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.207.3596.11021734.28451.1210159513.814.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.2416262.1346187475.303.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.30.26888.30000011122714571450000000581.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.21832.1433500207.767.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.30.25581.2014121717283919365953665.0.0.0.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.13616250.25529.1410548851.731.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.22154.1486126053.377.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.353.2807.1589500.18903.1415276055.705.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.1431432.1484932326.602.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/2.16.840.1.113662.4.1458149515632.1142444521.5908943698116625731.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.177.3596.7771142.23288.1185283544.464.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.43.66053.2016052608514947536024116.0.0.0.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.38818.105.1282163488.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.4120.7582168.13628.1385124590.565.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.36.162004.30000017101916014621800000015.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.22001.1411646030.637.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.410.6574342.2816289.26158.1495646347563.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.36.40608.2011022515471453729749123.0.0.0.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.276.0.45.1.7.3.161951842316.19040308135700253.94328.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.134.1762386377.1989.1244633271.163.100.200.306.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.1214597.1267542243.868.nii.gz
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.13616250.25608.1421752491.352.nii.gz

[plbenveniste]

Investigation into each image:

FILES_SEG:
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.5.1762879515.1876.1028546765.349.nii.gz # No problem on this image: the segmentation fails because of very thick slices (24mm)
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.207.3596.11021734.28451.1210159513.814.nii.gz # Large motion on slice 18. No impact on area of interest
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.2416262.1346187475.303.nii.gz # Large motion on slice 20. No impact on area of interest.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.30.26888.30000011122714571450000000581.nii.gz # Large motion on slice 17/19/21. No impact on area of interest. 
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.21832.1433500207.767.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.30.25581.2014121717283919365953665.0.0.0.nii.gz # Large motion on center of the image. Empty lesion mask.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.13616250.25529.1410548851.731.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.22154.1486126053.377.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.353.2807.1589500.18903.1415276055.705.nii.gz # Large motion on slices around 20. Just above the area of interest.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.1431432.1484932326.602.nii.gz # Large motion on slices around 20. No impact on area of interest.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/2.16.840.1.113662.4.1458149515632.1142444521.5908943698116625731.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.177.3596.7771142.23288.1185283544.464.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.43.66053.2016052608514947536024116.0.0.0.nii.gz # Large motion on slices around center slice. No impact on area of interest.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.38818.105.1282163488.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.4120.7582168.13628.1385124590.565.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.36.162004.30000017101916014621800000015.nii.gz # Large motion on slices around center slice just below area of interest
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.11880548.22001.1411646030.637.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.410.6574342.2816289.26158.1495646347563.nii.gz # Image with intensity spikes. Empty lesion masks
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.3.12.2.1107.5.2.36.40608.2011022515471453729749123.0.0.0.nii.gz # Large motion on slices around center slice. No impact on area of interest.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.276.0.45.1.7.3.161951842316.19040308135700253.94328.nii.gz # High contrast difference between lower part and upper part of the image. Lesion is located in top part where intensity is lower.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.134.1762386377.1989.1244633271.163.100.200.306.nii.gz # Slight motion on center slice
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.25.4.1214597.1267542243.868.nii.gz # Slight motion in center slice where lesion is located.
    - /home/GRAMES.POLYMTL.CA/p119007/critical_lesions/1.2.840.113619.2.244.3596.13616250.25608.1421752491.352.nii.gz # Image with intensity spikes. Empty lesion masks

[plbenveniste]

From this, we should discard images with intensity spikes and images where the segmentation files are empty.

@jcohenadad What should we do with the images where there is a large motion in center slices? This could prove problematic for spinal cord CSA computation for atrophy detection/computation.

[jcohenadad]

@jcohenadad What should we do with the images where there is a large motion in center slices? This could prove problematic for spinal cord CSA computation for atrophy detection/computation.

I would say, let's exclude them for now