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wasserth / TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images
Apache License 2.0
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All segmentations into 1 nifti #107

Closed abhi-vellala closed 1 year ago

abhi-vellala commented 1 year ago

Hello @wasserth,

Firstly, great work in making this tool. All the doctors are relying on its results and it is helping a lot in research communities. I see that, when we run totalsegmentator on one file, it generates masks for individual organs and saves them into each nifti file. Is there a way to combine all these results together and make 1 nifti file with all the segmentation masks? Thanks

wasserth commented 1 year ago

Hi, you can simply use the option -ml. This will save one nifti file containing all masks.

abhi-vellala commented 1 year ago

Okay. Perfect! It worked. Thank you. Closing the issue as it is sorted.