Segmentations of subtasks not working - heartchambers_highres, atrial_appendage_left

[lauraangeja]

Hi!

Thank you for having this repo available and organized!

I used TotaSegmentator on 100 cases, using two task commands, the heartchambers_highres and the total (--roi_subset = atrial_appendage_left). It didn't work in any of the ct scans for the atrial_appendage_left, pulmonary_artery and aorta. The stats.json of these structures is 0, and after visual inspection I also confirmed it. Do you know why this might be happening? { "heart_myocardium": { "volume": 117070.72748838365, "intensity": 164.7 }, "heart_atrium_left": { "volume": 96359.72849517316, "intensity": 490.17 }, "heart_ventricle_left": { "volume": 117325.70771960914, "intensity": 448.85 }, "heart_atrium_right": { "volume": 140172.68300115317, "intensity": 168.65 }, "heart_ventricle_right": { "volume": 178846.4075764194, "intensity": 179.89 }, "aorta": { "volume": 0.0, "intensity": 0.0 }, "pulmonary_artery": { "volume": 0.0, "intensity": 0.0 }, "atrial_appendage_left": { "volume": 0.0, "intensity": 0.0 } } This is a combined file of the statistics.json of both tasks.

I did:

echo "Processing file: $file_name"
TotalSegmentator -i "$file_path" \
                 -o "$file_output_dir" \
                 -ta heartchambers_highres \
                 --statistics 
                 

TotalSegmentator -i "$file_path" \
                 -o "$file_output_dir" \
                 --roi_subset $roi_subset \
                 --statistics         

[wasserth]

Does your image contain the original HU values or were the intensity ranges modified?