leaving this here for anyone who has trouble with the registration alignment as I did:
I had subtle registration misalignments that seemed to be influencing with my results, specifically in the anterior corpus callosum. I solved it by modifying the bspline registration file. Specifically, I increased the number of resolutions and decreased the FinalGridSpacingInVoxels values on the on the bspline registration parameter file to be:
This worked well for fixing the issue. The anterior corpus callosum in the reference file was being deformed downard into the autofluorescence striatum area. So the cells that should have mapped to deeper cortical layers near the motor/rostral cortex were mapping to middle cortical layers instead. This is subtle but I'm looking for modest effect sizes and it seemed to be more pronounced in the control condition over the mutant.
leaving this here for anyone who has trouble with the registration alignment as I did:
I had subtle registration misalignments that seemed to be influencing with my results, specifically in the anterior corpus callosum. I solved it by modifying the bspline registration file. Specifically, I increased the number of resolutions and decreased the FinalGridSpacingInVoxels values on the on the bspline registration parameter file to be:
This worked well for fixing the issue. The anterior corpus callosum in the reference file was being deformed downard into the autofluorescence striatum area. So the cells that should have mapped to deeper cortical layers near the motor/rostral cortex were mapping to middle cortical layers instead. This is subtle but I'm looking for modest effect sizes and it seemed to be more pronounced in the control condition over the mutant.