Small Animal and Ex Vivo Diffusion

Code, software, and datasets for small animal and ex vivo diffusion MRI

Here, we compile a list of existing and freely shared small-animl or ex vivo diffusion datasets (Table 1 and Table 2), a list of available software dedicated to image acquisition (Table 3), a list of software available for data pre-processing (Table 4), and a list of software available for model fitting (Table 5).

Citation of paper goes here

Small Animal Datasets

URL	Species	Diffusion Scheme	Other features	Institution
https://doi.org/10.14264/de9aa47	Mouse brain	DTI	Model of Concussion	University of Queensland
http://cmrm.med.jhmi.edu/ (M. Aggarwal et al. 2009)	Mouse brain	Atlas	Johns Hopkins

Ex Vivo Datasets

URL	Species	Diffusion Scheme	Other features	Institution
http://www.drcmr.dk/map-datasets	Mouse brain	micro-FA, Multi-shell, multi-resolution, Tractography, Axon diameter, Exchange rate, Axon relaxation	Validation: 3D synchrotron imaging of axons, cell bodies, vacoules and vessels, in vivo tracers	Danish Research Center for MR
https://www.nature.com/articles/sdata201672	Rat brain, rat spinal cord, human brain	DKI		Aarhus University
https://doi.org/10.1016/j.dib.2016.08.020	Rat, pig and human spinal cords	DTI	Ultra-high resolution (MR microscopy)	U of Florida
https://doi.org/10.1016/j.dib.2016.06.061	Rat brain	Multi-shell, high b-value	Mild chronic stress model	Aarhus University
https://github.com/sepehrband/AxonDiameter	Mouse brain	Multi-shell	Augmented with EM data and manually segmented axon diameter	U of Queensland
http://cmrm.med.jhmi.edu/ (M. Aggarwal et al. 2009)	Adult and postnatal developing mouse brains		Atlas	Johns Hopkins
https://doi.org/10.1016/j.neuroscience.2005.07.014	Mouse brain		Atlas	Several
http://doc.pmod.com/pneuro/pneuro.html?mousebrainatlasma-benveniste-mirrione4996.html	Cynomolgus, rhesus monkey and pig		Atlas	PMOD
https://osf.io/yp4qg/ (Cohen-Adad et al. 2019)	White matter axons		Microscopy data (non-MR)	Several
https://doi.org/10.1016/j.dib.2015.05.019	Cynomolgus macaque corpus callosum		Microscopy data (non-MR)	Several
http://www.duhs.duke.edu/mouseconnectome	Mouse Connectome in Waxholm Space	HARDI @ 43 um, 120 angle, b-value @ 4000 s/mm2	Segmented Atlas compared to retroviral tracers WHS Labels	Duke CIVM
https://civmvoxport.vm.duke.edu/voxbase/login.php?return_url=%2Fvoxbase%2Fstudyhome.php%3Fstudyid%3D754	Rat Connectome	MGRE @ 25 um HARDI @ 50 um 60 Angles Single specimen Average (n=6)b=3000 s/mm2	Segmented Atlas includes downloadable application for display	Duke CIVM
http://www.civm.duhs.duke.edu/rhesusatlas	Rhesus	MGRE@75um DTI@150 um 12 angles; b value =1500 s/mm2	Average N=10 241 labels	Duke CIVM
https://civmvoxport.vm.duke.edu/voxbase/login.php?return_url=%2Fvoxbase%2F	Mouse NODDI @ 50 um	8 shells B value 1000-8000 s/mm2 384 angles	With comparative histology	Duke CIVM
Histology: https://www.nitrc.org/projects/smatlas/ Atlas: https://www.nitrc.org/projects/validate29/	Squirrel monkey atlas + histology	Multi-shell HARDI acquisition	Atlas + histology	Vanderbilt

Data acquisition

Name	URL	Institution	Features	Dependencies
Pulse Sequences	https://osf.io/ngu4a/	University of Wisconsin Madison	Custom diffusion sequences (for Bruker Consoles)	ParaVision version
REMMI	https://remmi-toolbox.github.io/	Vanderbilt University	Sequences for small animal quantitative MRI including diffusion	Paravision or VNMRJversion
double PFG directions	https://remmi-toolbox.github.io/	Aarhus University	Output pairs of diffusion directions for dPFG	Matlab

Pre-processing

Name	URL	Institution	Features	Dependencies
DICOMIFIER	https://github.com/lamyj/dicomifier	University of Strasbourg	Conversion Bruker to DCM and NIFTI format (incl. Diffusion information)	Python
atlasBREX	https://github.com/jlohmeier/atlasBREX	Charité Berlin	Non-human brain extraction	FSL, AFNI, ANTs, ABSORB
PreQual	https://github.com/MASILab/PreQual	Vanderbilt	All pre-processing steps	Python
SCT	https://spinalcordtoolbox.com/	Polytechnique Montreal	Spinal cord MRI	Python
MChepato	https://github.com/fragrussu/MChepato	Vall d’Hebron Institute of Oncology	Tools for mouse liver dMRI-histology imaging used in (Grussu et al. 2022)	Python, FSL, QuPath, MRItools, DiPy, NiftyReg, and others
Tractoflow	https://doi.org/10.1016/j.neuroimage.2020.116889	Sherbrooked University	End to end tractography (not small animal specific)

Model Fitting

Name	URL	Models	Features	Dependencies
qMRINet	https://github.com/fragrussu/qMRINet	qMRI models	model fitting using fully-connected deep neural networks	NumPy/Nibabel/SciPy/PyTorch
Fast Kurtosis	https://cfin.au.dk/cfinmindlab-labs-research-groups/neurophysics/software/	Kurtosis metrics	kurtosis metrics from reduced diffusion kurtosis imaging data sets	Matlab