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- The DSURQE atlas was nonlinear warpped to DSI Studio's C57BL/6 space
- source: http://repo.mouseimaging.ca/repo/DSURQE_40micron/notes_on_DSURQE_atlas
- Based on the following atlases:
- * Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
- * Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
- * Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
- * Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.
- * Shannon Egan (2015) – added olfactory bulb segmentation based on data from the Allen Brain Institute
- * Lily Qiu (2016) – added the medial amygdala and medial preoptic area
- Compared to DSURE
- =================
- * added Medial amygdala (segmentated by Lily)
- * added Medial preoptic nucleus (segmented by Lily)
- --> these labels were mapped from the Dorr_2008 average (which was used for the segmentation) onto the
- 40 micron average. The segmentation should be cleaned up at some point
- (DSURE atlas notes) Compared to DSUR
- ====================================
- * olfactory layers segmented by Shannon Egan have been incorporated
- * all the old hippocampus labels (including the stratum granulosum and dentate gyrus) have been updated
- * voxels in the right side of the brain labeled as left have been fixed (same for the other way around)
- * spurious labeled voxels outside of the brain have been removed
- (DSUR atlas notes) Compared to DSU
- ==================================
- * Fixes in the hippocampus have been made from slice 200-240(ish). What still needs to be done in terms of the hippocampus are slices 199-151. This also means that there are voxels labeled:
- label value, name
- 6 , "TODO-fix-me-old hippocampus right"
- 13 , "TODO-fix-me-old stratum granulosum of hippocampus right"
- 16 , "TODO-fix-me-old dentate gyrus of hippocampus right"
- 63 , "TODO-fix-me-old stratum granulosum of hippocampus left"
- 66 , "TODO-fix-me-old dentate gyrus of hippocampus left"
- 106 , "TODO-fix-me-old hippocampus left"
- * Fixes were made to the boundary of the cortex (outside of the brain, and around the corpus callosum). These were roughly made in slices 199-233
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