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MouseSegmentation Pipeline

Pipeline: MouseSegmentation

Type: Rodent

Description: Skull-strips and segments mouse MRI

Source: UNC/JHU/SFU

Details:
The skull stripping uses the algorithm outlined in Automatic Skull-stripping of Rat MRI/DTI Scans and Atlas Building with the C57BL6 Brookhaven atlas.

The segmentation routine maps an atlas from Susumu Mori at JHU (see Complete Disruption of the Kainate Receptor Gene Family Results in Corticostriatal Dysfunction in Mice) using LDDMM as described in Multi-structure whole brain registration and population average. Optional N4 bias field correction may be performed on the skull-stripped image prior to registration.