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thalamicseg / hipsthomasdocker

Docker version of HIPS-THOMAS
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Fail cropping on 7T MP2RAGE data after updating #2

Open xingyu-liu opened 6 months ago

xingyu-liu commented 6 months ago

Hi,

Thank for developing the THOMAS, its very cool!

I'm running THOMAS for a 7T MP2RAGE T1w dataset. It worked perfectly previously, but after this following update, it miscrops thalamus with a part of thalamus unincluded (see attached pic, where part of LGN is missing).

Update 12/26/2023- a new container was uploaded to dockerhub ~ Dec 11 2023 which fixes some cropping errors for low quality T1 images. Please erase and redownload the docker image to use that

image

Any thoughs on this problem? Thank you very much!

Xingyu

anagrammarian commented 1 month ago

For skull stripped data, we found that regular cropping fails. Please download the new dockerhub container and try. docker pull anagrammarian/thomasmerged

I assume you are running the thomast1_hips wrapper.

anagrammarian commented 1 month ago

I see you are referencing the new container. Is this by any chance the AHEAD database data? It is best to run THOMAS on non-skull stripped data. I have noticed it fails there on a few cases as well. Also for MP2RAGE, the best way to run it is to synthesize the WMn from T1 maps and then run thomaswmn.