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add h2c function and --ct option

Taylor Hanayik requested to merge FEATURE/ct_bet into master

@mwebster, I have added a simple function to bet (and a new --ct option) that allows users to reliably skull strip CT images (which usually fail with traditional bet).

Could you please review? This eliminates the need for my old wrapper, and it's faster.

Here's the output of calling ~/fsl-dev/bin/bet2 test_ct.nii.gz h2c_ct.nii.gz --ct

result with new changes (GOOD):

Screenshot_2023-04-25_at_16.15.59

result with traditional bet2 with no --ct option (BAD):

image

The method is described here: https://pubmed.ncbi.nlm.nih.gov/22440645/ and here: https://github.com/neurolabusc/Clinical/blob/master/clinical_h2c.m

Edited by Taylor Hanayik

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