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Analysis software for MRI

Generic

SPM - Software package for the analysis of brain imaging data sequences
AFNI - A software suite primarily developed for the analysis and display of anatomical and fMRI data.
FreeSurfer - An open source software suite for processing and analyzing (human) brain MRI images.
FSL - A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Diffusion MRI

MRtrix3 - Advanced tools for the analysis of diffusion MRI data.
DIPY - a free and open source software project for computational neuroanatomy, focusing mainly on dMRI analysis

Pipelines

Nipype - provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
Automatic Analysis - multimodal MATLAB toolbox processing fMRI, DTI/DKI, and M/EEG
  • code repository
  • website
  • documentation
  • contact
  • programming language: {matlab}
  • tags: {MRI} {MEG} {EEG} {fMRI} {DTI} {DKI} {MATLAB}
  • paper
  • RRID:
  • tutorial:
    • URL
    • programming language: {matlab}
    • level: {beginner} / {intermediate}
    • tags: {PDF}
    • date:
    • duration:
    • by: Tibor Auer
fMRIPrep - A Robust Preprocessing Pipeline for fMRI Data

High-resolution

Nighres - Neuroimaging at high resolution
  • code repository
  • documentation
  • programming language: {python}, {java}
  • tags: {fMRI} {MRI}
  • paper
  • RRID: SCR_016287
  • tutorial:
  • URL
  • programming language: {python}
  • level: {beginner}
  • tags: {notebook}
  • by: the Nighres team

Misc

ANTs - To compute high-dimensional mappings to capture the statistics of brain structure and function
BrainSuite - A collection of open source software tools that enable largely automated processing of MRI of the human brain.
-   [website](http://brainsuite.org/)
-   documentation:
-   [contact](http://forums.brainsuite.org/)
-   programming language:
-   tags: 
-   paper DOI:
-   RRID:
-   tutorial
    -    [URL](http://brainsuite.org/tutorials/)
-   programming language:
-   level:
-   tags:
-   date:
-   duration:
-   by: