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McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
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extra GM volume IDPs generated if ROI mask indices not contiguous #123

Closed shen4brains closed 2 years ago

shen4brains commented 3 years ago

also GM volume outputs are in different order than matrix / parcellation look-up table

relevant code here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/3cebec9f0d26ddfb75b82ea7b5ae678a770eb505/bb_IDP/scripts/bb_IDP_T1_GM_parcellation#L41

possible solution may be to remove extra entries and reorder GM volume outputs to match parcellation after fslstats is run

shen4brains commented 3 years ago

also consider whether using the labelled GM image is a better input for fslstats than using parcel_to_T1 with a mask (<< this part assigned to @shen4brains)