Acquisitions

mouset2axial

T2-weighted image

labeledt2dsurqe

DSURQE Whole Brain Atlas

axialmouset2star

T2*-weighted image

axialrestingmouse

rsFMRI

Anatomical Pipelines

INC Anatomical Pipeline

The INC standard anatomical processing pipeline, includes: reorientation, affine alignment to common space, brain extraction, denoising, intensity bias correction, intensity scaling, and normalization to standard space(s).  Brain extraction includes a mix of automated methods including RATS-MM, BET, and 3dSkullStrip to find the best solution but often requires manual intervention as well which may increase the processing time and expense.

Anatomical Labeling

DSURQE Whole Brain Atlas

The native mouse brains are normalized to the DSURQE 70um template which is a whole brain T2 weighted high resolution average image of 40 postmortem c57 mice that are expertly labeled.  The labeling is a modified version of that outlined in the Dorr [1] paper with input from the following papers [2-6] as well.  Hence "D-S-U-R-Q-E"

Custom Atlas

Non-standard atlases can be implemented for your data for the INPC team. These must be pre-existing labelled brain images, any manual labelling must be billed separately. 

Manual Parcellation

Custom manual labelling of anatomical labelling for each session. Automated procedures that can provide partial mappings are first employed if possible, then manually altered or traced by 2 independent raters.

Voxelwise Maps

T2*

T2* processing involves estimating values by weighting and combining multiple acquisitions varying in echo time (TE), before coregistering to each participant/session native space and normalizing to template space.

Functional Pipelines

INC Resting State Pipeline

The INC standard functional pipeline includes reorientation, increasing voxel sizes by some scaling factor using fslchpixdim, Rician denoising, N4 bias field correction, rigid, affine, and nonlinear motion correction, brain extraction, registration to standard space, calculation of white matter and csf signals, and nuisance regression of appropriate regressors (e.g., motion, anatomical, etc). Label sets like DSURQE can then be overlaid on the functional data, and the timeseries of each label can be extracted. From this we can create whole brain connectivity matrices.

Diffusion Pipelines

INC Diffusion Pipeline

TBD

DSURQE Citations

[1] A.E. Dorr, J.P. Lerch, S. Spring, N. Kabani and R.M. Henkelman "High resolution three dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6j mice", NeuroImage 42(1):60-69, 2008.

[2] Steadman PE, Ellegood J, Szulc KU, Turnbull DH, Joyner AL, Henkelman RM, Lerch JP. Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas. Autism Res. 2014 Feb;7(1):124-37. doi: 10.1002/aur.1344. Epub 2013 Oct 22. PMID: 24151012; PMCID: PMC4418792.

[3] Ullmann JF, Watson C, Janke AL, Kurniawan ND, Reutens DC. A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. Neuroimage. 2013 Sep;78:196-203. doi: 10.1016/j.neuroimage.2013.04.008. Epub 2013 Apr 12. PMID: 23587687.

[4] Richards K, Watson C, Buckley RF, Kurniawan ND, Yang Z, Keller MD, Beare R, Bartlett PF, Egan GF, Galloway GJ, Paxinos G, Petrou S, Reutens DC. Segmentation of the mouse hippocampal formation in magnetic resonance images. Neuroimage. 2011 Oct 1;58(3):732-40. doi: 10.1016/j.neuroimage.2011.06.025. Epub 2011 Jun 17. PMID: 21704710.

[5] Qiu LR, Fernandes DJ, Szulc-Lerch KU, Dazai J, Nieman BJ, Turnbull DH, Foster JA, Palmert MR, Lerch JP. Mouse MRI shows brain areas relatively larger in males emerge before those larger in females. Nat Commun. 2018 Jul 5;9(1):2615. doi: 10.1038/s41467-018-04921-2. PMID: 29976930; PMCID: PMC6033927.

[6] Beera KG, Li YQ, Dazai J, Stewart J, Egan S, Ahmed M, Wong CS, Jaffray DA, Nieman BJ. Altered brain morphology after focal radiation reveals impact of off-target effects: implications for white matter development and neurogenesis. Neuro Oncol. 2018 May 18;20(6):788-798. doi: 10.1093/neuonc/nox211. PMID: 29228390; PMCID: PMC5961122.