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DSURQE.note.txt

DSURQE.note.txt 2.3 KB
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  1. The DSURQE atlas was nonlinear warpped to DSI Studio's C57BL/6 space
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  4. source: http://repo.mouseimaging.ca/repo/DSURQE_40micron/notes_on_DSURQE_atlas
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  5. Based on the following atlases:
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  6. * Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
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  7. * Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
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  8. * Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
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  9. * Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.
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  10. * Shannon Egan (2015) – added olfactory bulb segmentation based on data from the Allen Brain Institute 
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  11. * Lily Qiu (2016) – added the medial amygdala and medial preoptic area
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  13. Compared to DSURE
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  14. =================
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  15. * added Medial amygdala (segmentated by Lily)
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  16. * added Medial preoptic nucleus (segmented by Lily)
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  17. --> these labels were mapped from the Dorr_2008 average (which was used for the segmentation) onto the 
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  18.     40 micron average. The segmentation should be cleaned up at some point
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  20. (DSURE atlas notes) Compared to DSUR
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  21. ====================================
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  22. * olfactory layers segmented by Shannon Egan have been incorporated
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  23. * all the old hippocampus labels (including the stratum granulosum and dentate gyrus) have been updated
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  24. * voxels in the right side of the brain labeled as left have been fixed (same for the other way around)
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  25. * spurious labeled voxels outside of the brain have been removed
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  26. 

  27. (DSUR atlas notes) Compared to DSU
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  28. ==================================
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  29. * 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:
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  30. 

  31. label value, name
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  32. 6          , "TODO-fix-me-old hippocampus right"
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  33. 13         , "TODO-fix-me-old stratum granulosum of hippocampus right"
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  34. 16         , "TODO-fix-me-old dentate gyrus of hippocampus right"
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  35. 63         , "TODO-fix-me-old stratum granulosum of hippocampus left"
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  36. 66         , "TODO-fix-me-old dentate gyrus of hippocampus left"
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  37. 106        , "TODO-fix-me-old hippocampus left"
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  38. 

  39. * 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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  40.