Resources

Please note that this resources are not exhaustive.

MRI physics

• IMAIOS e-MRI: basic online course about MRI
• Questions and Answers in MRI: advanced information about MRI

General information about neuroimaging studies

• Article: Recommendations for the implementation of multicenter studies with MRI (in French)
• Article: Longitudinal multi-centre brain imaging studies: guidelines and practical tips for accurate and reproducible imaging endpoints and data sharing

Network

• REMI: French multicenter MRI network ("Réseau d'Entraide Multicentrique en IRM").

MRI Quality Control

• mriqc: quality control of functional fMRI and structural (T1w and T2w) data, extraction of no-reference IQMs (image quality metrics). See also here
• VisualQC : assessing and assuring the quality of imaging data, be it an raw acquisition (fMRI run or T1w MRI) or an automatic segmentation (be it gray or white surfaces for cortical thickness, or a subcortical segmentation) requires visual inspection manually.

Data sharing and data format

• openNeuro: a free platform to share BIDS-compilant data.
• ida loni: access to several database such as ADNI, ABIDE, PMI
• BIDS: a standardized format for organizing and describing neuroimaging data and study outputs. See also here
• dcm2niix: conversion of DICOM into NIfTI format (and with a json file for each NIfTI).

Data Viewer

• Anatomist: data visualization and library of high-level neuroimaging graphical components.
• FSLeyes: image viewer.
• mrview: MRTrix image viewer

General information about neuroimaging software

• Neuroimaging Tools & Resources Collaboratory (NITRC) : a website that offers comprehensive information on an ever expanding scope of neuroinformatics software and data. You can find a lot of software and useful link in the Resources Registry part.
• Neurostars : a question and answer forum for neuroscience researchers, infrastructure providers and software developers.

Software suite

• BrainVisa: neuroimaging software platform for mass data analysis. Contains software as Morphologist (brain segmentation and sulcal analysis)
• populse_mia: image processing environment mainly targeted at the analysis and visualization of large amounts of MRI data.
• Nipype: a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., ANTS, SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer, DIPY)

Functional MRI

• Andy's Brain Book and Andy's brain videos: tutorial abour fMRI processing and others neuroimaging tools
• mumforbrainstats: video about fMRI processing by Jeanner Mumford
• pratciCal fMRI blog: a blog with tips about fMRI
• Analysis principles - Unviversity of Cambridge: a blog with tips about fMRI analysis (and SPM)
• SPM tutorial: tutorial to analyse fMRI dataset with SPM

Diffusion MRI

• Andy's Brain Book: tutorial about diffusion processing with MRTrix
• B.A.T.M.A.M tutorial: tutorial about diffusion processing (tractography) with MRTrix
• MRTrix user documentation with many explanations

Spectroscopy

• MRShub: collection of resources for magnetic resonance spectroscopy