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Add spinal cord segmentation and intervertebral disc levels to the template #11

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jcohenadad opened this issue Dec 6, 2023 · 3 comments
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@jcohenadad
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Context: https://forum.spinalcordmri.org/t/integrating-dog-template/1179

In order to be used as a replacement to the PAM50 template, the dog template should come with:

  • templatedog_t1w.nii.gz: The current T1w template
  • templatedog_t2w.nii.gz: The current T2w template
  • templatedog_cord.nii.gz: a spinal cord segmentation (equivalent to PAM50_cord.nii.gz)
  • templatedog_label_disc.nii.gz: intervertebral discs (equivalent to PAM50_label_disc.nii.gz)
  • templatedog_levels.nii.gz: spinal cord segmentation labeled for vertebral level (equivalent to PAM50_levels.nii.gz)
  • info_label.txt: TXT file describing each file present in the template package. This file is used by sct_register_to_template

Once generated, these files should be packaged inside a template folder, and that folder should be enclosed into another folder called templatedog, and then zipped and uploaded as a release asset. See latest PAM50 release for inspiration.

@rohanbanerjee
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I'm uploading the files for the template one by one. The below is the qc for the templatedog_label_disc.nii.gz
qc_dog_template_disc_levels.zip

Uploading the other required files asap.

@rohanbanerjee
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Added all required files in the latest release (r20240112): https://github.com/spinalcordtoolbox/template-dog/releases/tag/v2.0

@jcohenadad
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@rohanbanerjee there were issues with your files #12 #13.

Next time you create a release, please consult with me before publishing the release.

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