Manual segmentation of MS lesions in the spinal cord to be reviewed by neuroradiologist

[plbenveniste]

Creating this issue to centralize all images which are tricky to annotate and which could be discussed with a neurologist.

Tagging @Nilser3

[plbenveniste]

This is image from CanProCo is tricky : sub-tor016_ses-M0_PSIR.nii.gz

Should the spinal cord central canal be segmented or not ? How many lesions should be counted ? Also the M12 image has a lot more lesions, did we miss some ?

Note

Code to get image : fsleyes sub-tor016/ses-M0/anat/sub-tor016_ses-M0_PSIR.nii.gz sub-tor016/ses-M0/anat/sub-tor016_ses-M0_T2w.nii.gz derivatives/labels/sub-tor016/ses-M0/anat/sub-tor016_ses-M0_PSIR_lesion-manual.nii.gz &
Code to get M12 image : fsleyes sub-tor016/ses-M12/anat/sub-tor016_ses-M12_PSIR.nii.gz sub-tor016/ses-M12/anat/sub-tor016_ses-M12_T2w.nii.gz derivatives/labels/sub-tor016/ses-M12/anat/sub-tor016_ses-M12_PSIR_lesion-manual.nii.gz &

[plbenveniste]

This case is not that easy as well to know if it's one big lesion or multiple lesions : Canproco - sub-tor029_ses-M0_PSIR.nii.gz

Note

Code to get image : fsleyes sub-tor029/ses-M0/anat/sub-tor029_ses-M0_PSIR.nii.gz sub-tor029/ses-M0/anat/sub-tor029_ses-M0_T2w.nii.gz derivatives/labels/sub-tor029/ses-M0/anat/sub-tor029_ses-M0_PSIR_lesion-manual.nii.gz &

[plbenveniste]

In this case, lesions have been annotated with multiple values (1 and 2). One theory is that the annotation comes from the level of confidence of the lesion annotation. Subject : sct-testing-large - sub-rennesMS002_acq-sagcerv_T2w.nii.gz

The lesions in yellow could be focal lesions ? Dirty white matter ?

Note

Code to get image : fsleyes sub-rennesMS002/anat/sub-rennesMS002_acq-sagcerv_T2w.nii.gz sub-rennesMS002/anat/sub-rennesMS002_acq-inf_T2star.nii.gz derivatives/labels/sub-rennesMS002/anat/sub-rennesMS002_acq-sagcerv_T2w_lesion-manual.nii.gz &