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Extend C1 vertebrae on the PAM50_levels template file #20

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jcohenadad opened this issue Jan 13, 2023 · 1 comment · Fixed by #21
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Extend C1 vertebrae on the PAM50_levels template file #20

jcohenadad opened this issue Jan 13, 2023 · 1 comment · Fixed by #21

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@jcohenadad
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jcohenadad commented Jan 13, 2023 •
edited by joshuacwnewton
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Context: https://forum.spinalcordmri.org/t/c1-vertebral-level-labelling/1002/3

Ah! OK, another reason for C1 to be cropped if the cord segmentation spans it entirely would be because it is difficult to find the top part of C1, hence the algorithm was trained to stop after a given distance that is based on the length of C1 in the PAM50 template (which is cropped):

Historically, no user was interested in looking at C1, hence it was somewhat “neglected”, but I agree we should extend the segmentation on the PAM50 template so that the vertebral labeling would be more correct regarding C1 level.
@mguaypaq mguaypaq mentioned this issue Jan 18, 2023
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@joshuacwnewton joshuacwnewton mentioned this issue Jan 27, 2023
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@joshuacwnewton joshuacwnewton mentioned this issue Feb 14, 2023
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@jcohenadad jcohenadad transferred this issue from spinalcordtoolbox/spinalcordtoolbox Aug 4, 2023
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We should probably extend the coverage up to slice 985, which corresponds to the top of C1:

image

jcohenadad added a commit that referenced this issue Aug 4, 2023
@jcohenadad
Have the top of C1 spinal and vertebral correspond
863d154 
See: #20 (comment)
@jcohenadad jcohenadad mentioned this issue Aug 5, 2023
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@jcohenadad jcohenadad changed the title Extend C1 vertebrae on the PAM50 template Extend C1 vertebrae on the PAM50_levels template file Aug 5, 2023
jcohenadad added a commit that referenced this issue Aug 5, 2023
@jcohenadad
Add script to update the PAM50_levels.nii.gz file
9c14401 
Related to #20
jcohenadad added a commit that referenced this issue Aug 5, 2023
@jcohenadad
Extend rostral and caudal coverage of PAM50_levels
0b32914 
Fixes #20
jcohenadad added a commit that referenced this issue Oct 23, 2023
@jcohenadad
Update spinal levels based on Frostell et al. paper (#18)
f4b3666 
* Getting started with a script to compute spinal segments

* First version of 'working' code

* Added .gitignore

* Completed list of percent spinal cord

* Added some printouts for the user

* Added some checks

* Zero values above z_top

* Fixed "__setitem__" method not defined on type "uint8"

* Have the top of C1 spinal and vertebral correspond

See: #20 (comment)

* Removed hard-coded values

* Cleanup

* Adding new spinal levels

* Removed PAM50/spinal_levels

* Fixed cumulative error caused by rounding

#18 (comment)

* Added backbone code to create PAM50_spinal_midpoint.nii.gz

* Fixed wrong value for midpoint

* Added midpoint labels

* Updated info_label.txt

* Changed dtype for UINT8
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Update PAM50_cord.nii.gz spinal cord segmentation spinalcordtoolbox/PAM50
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