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McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
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multichannel FAST tissue segmentation output filenames inconsistently assigned to different tissue classes #124

Closed shen4brains closed 3 years ago

shen4brains commented 3 years ago

This is only an issue when T2s are added to the tissue classification, which is currently implemented in the Cam-CAN_multiChannelFAST branch.

Relevant codeblock starts here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/cc60f6288654793993d066772cca18bedd92a447/bb_structural_pipeline/bb_struct_init#L152

Where T1_brain_pve_0.nii.gz and T1_brain_pve_1.nii.gz are reversed in some subjects so assignment of WM and GM become reversed.

Possible solution is to first check the mean intensity of each tissue class by applying each "pve.nii.gz" mask to the T1 and re-name the 'pve' files as needed.