Create coarse masks associated with classes from TotalSegmentator

neuropoly / totalspineseg

Segmentation of vertebrae, intervertebral discs, spinal cord and CSF from MRI images.

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Create coarse masks associated with classes from TotalSegmentator #2

Closed jcohenadad closed 7 months ago

jcohenadad commented 1 year ago

Few considerations:

How masks are done
- Under 3D Slicer, open MPRAGE, draw 'blob' covering regions, making sure to cover the various intensity range of the structure (in case it is a large structure subjected to bias field inhomogeneity).
- Save each class as a nii.gz file.
Classes not visible on the MRI
- Ignore. Start with structures that are visible.
Naming/organization of the masks
- use the same naming as TotalSeg. Example: organ_spleen.nii.gz, vertebrae_L3.nii.gz
Location of files: upload to shared google folder.

Once done, move this text in the README. That will be useful for the future paper.

yw7 commented 1 year ago

I uploaded the masks to this Google Drive folder and the output statistics to this file under 'data\derivatives\manual_masks'. The following masks are not clearly visible in the image and I left them empty: colon duodenum face femur_left femur_right gluteus_maximus_left gluteus_maximus_right gluteus_medius_left gluteus_medius_right gluteus_minimus_left gluteus_minimus_right hip_left hip_right humerus_left humerus_right iliac_artery_left iliac_artery_right iliac_vena_left iliac_vena_right organ_gallbladder organ_pancreas small_bowel urinary_bladder

yw7 commented 1 year ago

What should be the next step? should I make masks for another Image? or this image is enough for now? Thanks

jcohenadad commented 1 year ago

Let's see what results we get with this sets of label statistics for now.