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DCAN-Labs / BIBSnet

This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can easily be included in other processing pipelines and for circumventing JLF within Nibabies.
https://bibsnet.readthedocs.io/en/latest/
Apache License 2.0
4 stars 8 forks source link

Add more documentation on how brain-z-size is calculated #93

Closed LuciMoore closed 2 months ago

LuciMoore commented 11 months ago

A short summary of what you would like to see in BIBSnet.

Include:

  1. the lookup table for average head radius per age (copied here at end of message)
  2. how/where brain z size is calculated from lookup table (eg here)

Could also consider including the brain-z-size in lookup table itself in order to provide a quicker reference for people troubleshooting and simplify the code. It's currently unclear which brain-z-size to use because you have to hunt down what was used as default. Could also adding logging to make this more clear as well

Current LUT referenced in code: Candidate_Age(mo.) Head_Radius(in.) 0 2.264376953 1 2.240901599 2 2.538989445 3 2.582607262 4 2.689976627 5 2.696930247 6 2.754071188 7 2.796856988 8 2.868104704 9 2.857207413 10 2.870473081 11 2.927566759 12 2.912491854 13 3.05646866 14 2.956881813 15 3.037642612 16 2.962304536 17 2.992813212 18 3.055306805 19 3.052238131 20 3.124742049 21 2.927920436 22 3.053020303 23 3.070852744 24 3.092992679 25 3.09609416 26 3.219376827 27 2.802895387 28 3.594249131 29 3.094679449 30 3.58098622 31 3.048811879 32 3.195663726 33 3.205203715 34 3.211614122 35 3.194467072 36 3.196361774 37 3.112615958 38 3.135352379 39 3.111479137 40 3.123415758 42 3.175936889 43 3.119436885 44 4.034577807 45 3.183098862 46 3.130047214 47 3.242781965 48 3.276602391 49 3.335357091 52 3.265859432 53 3.328990893 54 3.390000288 55 3.415199821 56 3.286549575 57 3.183098862 60 3.713615339 65 3.25869746 67 3.023943919 68 3.055774907 70 3.342253805 136 2.944366447 470 3.333411864

Do you have any interest in helping implement the feature?

No :(

Add any additional information or context about the request here.

No response

LuciMoore commented 2 months ago

closing for now as this documentation will no longer be included after anticipated updates currently under development for image cropping