add subjects to exclude from sub-1000032 to sub-1025290

sct-pipeline / ukbiobank-spinalcord-csa

Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.

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add subjects to exclude from sub-1000032 to sub-1025290 #49

Closed sandrinebedard closed 3 years ago

sandrinebedard commented 3 years ago

Description

This PR adds images to exclude from the analysis to exclude.yml from what Étienne observed in the QC report from the first 350 subjects of UK Biobank. It refers to subjects from sub-1000032 to sub-1025290.

I looked at all images and the main issue is still shading of the spinal cord in T2w images (see issue #45 )

jcohenadad commented 3 years ago

I looked at all images and the main issue is still shading of the spinal cord in T2w images (see issue #45 )

this is due to the poor S-I coverage of the receive coil used for these subjets.

sandrinebedard commented 3 years ago

this is due to the poor S-I coverage of the receive coil used for these subjets.

Ahh I see! And why would it only be the case for T2w images for those subjects? Not the same coil is used for T1w and T2w acquisitions?

jcohenadad commented 3 years ago

this is due to the poor S-I coverage of the receive coil used for these subjets.

Ahh I see! And why would it only be the case for T2w images for those subjects? Not the same coil is used for T1w and T2w acquisitions?

ah! excellent point. Two possible explanations:

my diagnosis was wrong and the issue was not the coil but the fact that the T2w image is a 3D sequence (do you confirm it is?), with one of the phase encoding along the S-I direction and with the excitation profile being very restrictive in the S-I direction
it is possible (although unlikely) that the selected coil elements were different between the T1w and the T2w scans (ie: for the T2w scan, for some reasons, the neck coil elements were not selected). But again, I think this scenario is quite unlikely.

sandrinebedard commented 3 years ago

this is due to the poor S-I coverage of the receive coil used for these subjets.

Ahh I see! And why would it only be the case for T2w images for those subjects? Not the same coil is used for T1w and T2w acquisitions?

ah! excellent point. Two possible explanations:

my diagnosis was wrong and the issue was not the coil but the fact that the T2w image is a 3D sequence (do you confirm it is?), with one of the phase encoding along the S-I direction and with the excitation profile being very restrictive in the S-I direction

it is possible (although unlikely) that the selected coil elements were different between the T1w and the T2w scans (ie: for the T2w scan, for some reasons, the neck coil elements were not selected). But again, I think this scenario is quite unlikely.

Yes it is a 3D sequence, this is the info I have on the T2w FLAIR acquisition: