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Orientation problem labels-disc M12 subjects #71

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plbenveniste opened this issue Oct 25, 2023 · 4 comments
Closed

Orientation problem labels-disc M12 subjects #71

plbenveniste opened this issue Oct 25, 2023 · 4 comments
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@plbenveniste
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plbenveniste commented Oct 25, 2023

I identified an orientation problem in the sub-van111_ses-M12_PSIR_lesion-manual_label.nii.gz.

The dimension is : (16, 336, 336) instead of (336, 336,16)

→ Currently investigating how to solve and if other files have the same problems

The files come from "Discs labelling Hourglass"

tagging @NathanMolinier @valosekj

@plbenveniste plbenveniste self-assigned this Oct 25, 2023
@valosekj
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Good catch!

The original PSIR image looks good (it has 336, 336, 16 dimensions; which also corresponds with M0):

valosek@macbook-pro:~/data/data.neuro.polymtl.ca/canproco/sub-van111$ sct_image -i ses-M12/anat/sub-van111_ses-M12_PSIR.nii.gz -header | grep "dim"
dim		[3, 336, 336, 16, 1, 1, 1, 1]

valosek@macbook-pro:~/data/data.neuro.polymtl.ca/canproco/sub-van111$ sct_image -i ses-M0/anat/sub-van111_ses-M0_PSIR.nii.gz -header | grep "dim" 
dim		[3, 336, 336, 16, 1, 1, 1, 1]

Maybe the disc labeling was done on the reoriented image? If so, try to reorient sub-van111_ses-M12_PSIR_lesion-manual_label.nii.gz to the PSIR native orientation (AIL).

@NathanMolinier
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Indeed the images were reoriented before creating the labels and I forgot to reuse the original orientation of the image.

However, it is a good reminder that we always need to make sure that we check the orientation before treating an image. The class Image (from SCT) is suited for this task.

@valosekj
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Okay, I see! Could you please reorient the disc labels back to the original orientation and push them to git-annex?

@plbenveniste
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This was solved during the re-orientation of all derivatives file in this issue : ivadomed/ms-lesion-agnostic#1 (comment)

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