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fepegar / highresnet

PyTorch implementation of HighRes3DNet
MIT License
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highresnet sometimes outputs a value of 20 or 21 which are not in GIFNiftyNet.ctbl #37

Closed paul-reiners closed 3 years ago

paul-reiners commented 3 years ago

Description

highresnet sometimes outputs a value of 20 or 21 neither of which are in GIFNiftyNet.ctbl.

What brain region do 20 and 21 stand for?

What I Did

Ran highresnet on a NIFTI file.

fepegar commented 3 years ago

I don't have an answer for this.

Maybe @wyli or @res191 can help.

wyli commented 3 years ago

do they refer to the 19th/20th (zero-indexed) line of GIFNiftyNet.ctbl ? which means 23 Right-Hippocampus and 24 Left-Hippocampus.

fepegar commented 3 years ago

do they refer to the 19th/20th (zero-indexed) line of GIFNiftyNet.ctbl ? which means 23 Right-Hippocampus and 24 Left-Hippocampus.

I don't think so. The hippocampus seems fine.

I ran the example in the README of this repo and got no voxels labeled as 20. These are the ones labeled as 21:

Screenshot

Maybe some of the labels marked in GIF as "non-brain" or something similar got remapped to 20 and 21.

fepegar commented 3 years ago

It's probably "non-ventricular CSF".

Anyway, @paul-reiners I think you can safely ignore the labels that are not present in the color table and consider them background.

wyli commented 3 years ago

alright... waded through the 2017 backup files maybe they mean 20 Right-Cerebral-Exterior 21 Left-Cerebral-Exterior

fepegar commented 3 years ago

Thanks for the archeology! It does sound like those structures can be safely ignored then. Is that ok, @paul-reiners?

paul-reiners commented 3 years ago

Yes, that's okay. Thanks for taking the time to look into this.