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sina-mansour / UKB-connectomics

This repository will host scripts used to map structural and functional brain connectivity matrices for the UK biobank dataset.
https://www.biorxiv.org/content/10.1101/2023.03.10.532036v1
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Adding mtnormalise #5

Closed sina-mansour closed 2 years ago

sina-mansour commented 2 years ago

Following on the suggestion by @Lestropie (this commit):

RS: Currently missing from here is the mtnormalise command. I do not know the extent to which the UKB pre-processing deals with the B1 bias field, as many models perform all computations relative to the b=0 image intensity, and therefore a multiplicative bias field is irrelevant; but for AFD it is highly critical. I would suggest just using the mtnormalise command as-is here. It is however worth checking the quality of the brain masks in some exemplar subjects: inclusion of non-brain voxels in the mask here can be highly detrimental: https://github.com/MRtrix3/mrtrix3/issues/1973 So unlike the mask used for CSD above, where a generous mask is preferable, here a more conservative mask is preferable; indeed it may be preferable to erode the mask slightly for mtnormalise.

sina-mansour commented 2 years ago

I've now added mtnormalise (https://github.com/sina-mansour/UKB-connectomics/commit/ff13ef5281bf467534fa721dc6bbbdbedd6c8c70) and it does visually improve the wm fod:

wm_fod

image

wm_fod_norm (after mtnormalise)

image