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rabies

fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/en/stable/

rat_rsfmri_preprocessing

Preprocessing toolbox for rat rs-fMRI data

reorient

A tool for reorienting and cropping MRI data

riciannet

MRI denoising used RicianNet

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:

rodent-whole-brain-preprocessing-recipe

A generally applicable whole-brain preprocessing toolbox for mice and rats

rodentmriskullstripping

U-Net based automatic Rat brain-mask Segmentation tool, developed by Hsu

sammba-mri

small mammals brain MRI

samri

Small Animal Magnetic Resonance Imaging via Python.

sashimi

SASHIMI segmentation is a Matlab App for semi-automatic interactive segmentation of multi-slice images.

sharcq

Tools to register histological section images and cell count locations to mouse brain atlas

sherm-rodentskullstrip

Implementation of algorithm in 'Yikang Liu et al. (2020) Automatic Brain Extraction for Rodent MRI Images. Neuroinformatics. doi: 10.1007/s12021-020-09453-z''

simpleelastix

Multi-lingual medical image registration library

skullstripping2023

MATLAB code to provide a GUI based tool for Skull Stripping from Axial MRI Skull Scans

spmmouse

SPMMouse ongoing maintenance effort

spmscripts

Handy scripts for SPM

structuralfunctionaljointregistration

a test example for jointly using structural and functional MRI to guide registration

synapselocator

Perform registration of 3D imaging data and localization of spots (synapses/boutons) in semi-automatic mode (with graphical user interface).

tissueweightedmean

vaa3d_tools

www.vaa3d.org

verse-mb

virtual-scanner

An end-to-end hybrid MR simulator/console

voxelbasedmorphometrydemo

MATLAB demo of Voxel Based Morphometry (VBM), using SPM12.

voxelmorph

Unsupervised Learning for Image Registration

voxelstats

A MATLAB package for multi-modal voxel-wise brain image analysis

z-cw

Simulation of Z-spectra values for continous wave (cw) irradiation

z-psl

Simulation of Z-spectra values for pulsed spinlock (pSL) irradiation