Mouse Imaging Centre, Hospital for Sick Children, Toronto Canada

pydpiper

Python code for flexible pipeline control

RMINC

Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:

pyminc

A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch

minclaplace

Laplace's equation for measuring thickness (or other uses of streamlines) between two boundaries

minc-stuffs

Scripts and bits of code for minc files.

brain-view2

MRIcrotome

R package for MRI data visualization

generate_deformation_fields

Given an input Jacobian determinant, this code will generate a deformation field that produces that Jacobian field. (Made for MINC format files)

Scinet-SS-bayesian-neuroimaging-R

Slides for the Scinet Summer School session on bayesian analysis of neuroimaging data with R and Stan

fastCell

Fast Deep Neural Networks for Cell Image Analysis

mice-nix-overlay

Nix expressions for installing some MINC-related medical image processing software

mice-apptainer

Singularity container definition for MICe/Oxford neuroimaging software

MICe-lab

Scripts and pipelines that are specific to the Mouse Imaging Centre lab. These programs are not very likely to be applicable to other centres.

neuronix

Use the Nix package manager to build imaging pipelines

.github

Canonical repository for organization-wide README.md.

blog

dcm2bids-conversion

Wrapper package for dcm2bids to convert POND and KIND dicom directories to BIDS

mice-spack-packages

Spack packages of MICe software (and some external dependencies)

minc-scripts

various scripts processing minc files or minx-associated files

minc-toolkit-containers

Making containers with minc-toolkit

minc-toolkit-v2

Version 2 of the minc-toolkit, uses tools based on ITK version 4.x

MINC-VM

Packer built VMs with minc-toolkit and friends

MINC.jl

Julia bindings for the MINC medical imaging library (libminc2)

minc2-simple

simplified MINC2 API

mincModelExplorer

Mouse-Imaging-Book

A book detailing how do an end-to-end mouse imaging analysis

pydpiperQC

RMINC-test-data

Data files for running RMINC tests

scanbaseTools

Tools for uploading and interacting with scanbase

tissue_vision_tools