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3dmprageise

Super nifty AFNI script to MPRAGEise your MP2RAGEs

ants

Advanced Normalization Tools (ANTs)

antspy

Advanced Normalization Tools in Python

antsregistration-maget

A reimplementation of MAGeTbrain using only ANTs tools.

argparse-bash

Use python's argparse module in shell scripts

atlases

Segmentations of Neuroanatomy on Hi-Res T1 and T2 MRIs and publicly available population averages in MNI space

autosusan

Structure-preserving denoising using FSL's SUSAN

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

bto_mri_protocols_info

This is a repository of wiki, code and containers for post-processing data acquired using the BRAIN-TO imaging protocols on a Siemens Prisma 3 T

cni_toolbox

conp-dataset

:open_file_folder: A DataLad dataset for CONP

docker_pyprf

Dockerfile for PyPRF

faceoff

ANTs-based commandline utilities for (1) consistent, super-fast defacing of anatomical MRI images (2) dielectric pad masking

greedy_c3d_binaries

Binaries for greedy and c3d tools

habenula_segmentation

Myelin content based human habenula segmentation from anatomical MRI

hcppipelines

Processing pipelines for the HCP

iterativen4_multispectral

A pipeline which performs iterative classification and bias field correction of T1-weighted MRIs

laynii

Stand alone fMRI software suite for layer-fMRI analyses.

laynii_extras

Auxiliary scripts, bits & pieces built around LayNii

minc-toolkit-extras

Extra miscellaneous scripts for minc-toolkit

mp2rage-related-scripts

MP2RAGE Scripts - T1 map correction & Background noise removal

mp2rage-utils

User-friendly MP2RAGE scripts with a single YAML input.

mp2rager

mp2rageR is an R implementation based off of MATLAB code made publicly available by José P. Marques. See vignettes for help.

multibrain

A list of brain imaging datasets with multiple scans per subject. Feel free to update the list via 'pull requests'!

multishell-qspace-gradients

Generate a ready-to-import gradient table for a multi-shell DWI acquisition using Emmanuel Caruyer et al., 2013 uniform schemes in a Siemens scanner.

optimized_antsmultivariatetemplateconstruction

A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support

presurfer

Scripts to prepare MP2RAGE for Freesurfer

pymp2rage

Lightweight Python package to process MP2RAGE and ME-MP2RAGE-data

srikash.github.io

Personal Website

surf_laynii

Script that enables LAYNII layering using Freesurfer segmentations