A page of information and resources on functional MRI.
Suggestions welcome! Either submit an issue or contact me (jpyles at cmu dot edu).
Useful Websites
Software
Brain Anatomy
- fMRI 4 Newbies - Jody Culham's excellent site for intro fMRI info
- Berkeley 3T Training Guide - This is by far the most useful single document I have found for understanding MRI parameters and Siemens scanners. Written by Berkeley's MR physicist Ben Inglis (who also writes practiCal fMRI) it is a must read.
- practiCal fMRI - Ben Inglis' blog on everything related to MRI physics (especially Siemens magnets) and lots on fMRI practice and other issues. An excellent resource.
- NIH MRI Summer Course - A great collection of lecture videos and slides covering many aspects of functional and structural imaging.
- MIT Imaging Mindhive - A wiki of very good information on various aspects of fMRI.
- Harvard Center for Brain Science FAQ - Very good MRI FAQ.
- Beauchamp Lab Wiki - Michael Beauchamp has an excellent lab wiki with lots of useful info.
- Aguirre Lab - Useful resources from Geoff Aguirre's lab website at Univ. of Pennsylvania.
- UCSD Fundamentals of Functional Neuroimaging Course - Excellent complete fMRI course that is online from Tom Liu.
- SDSU Foundations of Neuroimaging Course - A technical and excellent course on MRI from Marty Sereno.
Other Useful General Research Sites
- Data Analysis Tips I Wish I'd Known Sooner - A good set of tips.
- Lab Hacks - Good general advice on research for grad students and others from Patrick Beukema at CMU.
- Jody's Advice to Young Scientists - Another excellent collection of general research advice from Jody Culham at Western University.
Main fMRI Software Packages
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SPM - The most widely used fMRI analysis software. Based in Matlab it is powerful and versatile, but has poor visualization capabilities. (From: FIL at Univ. College London)
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AFNI - An excellent and fast Linux/Unix compiled analysis package with scripting capability and good visualization, especially when combined with the SUMA surface analysis package. (From: Medical College of Wisconsin and now based at NIH)
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FSL - Another excellent Linux/Unix compiled package with good visualization and powerful analysis and scripting capabilities. FSL also is also home to one of the standard diffusion MRI packages. (From: FMRIB, Univ. of Oxford)
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BrainVoyager - A powerful cross platform compiled package with excellent visualization and surface analysis capabilities and an easy to use GUI. Requires a paid license. (From: Rainer Goebel and Brain Innovations, Maastricht, The Netherlands)
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FreeSurfer - An analysis package rooted in surface reconstruction.
recon-allis the standard automatic segmentation routine for many researchers, even if they analyze their data in other packages. (From: The Laboratory for Computational Neuroimaging and the Martinos Center at MGH) -
MrVista - The analysis package developed by Brain Wandell's Vista Lab based in Matlab (with compiled portions) and optimized for surface analysis and vision science experiments. (From: VISTA Lab, Stanford)
Other Useful MRI Software
- NeuroDebian - A repository for lots of neuroimaging software and an easy way to install many useful packages such as AFNI, FSL, etc.
- MriCron - Probably the standard cross-platform NIfTI viewer. Also includes the dcm2nii converter.
- NeuroElf - Excellent and powerful set of tools, functions, and a GUI interface that allows many formats of fMRI data to be imported and exported from Matlab. There are also tools for pre-processing and analysis. (Written and maintained by Jochen Weber at Columbia University.)
- NIPY - Python tools for neuroimaging.
- Nipype - Python project to integrate different neuroimaging software packages. (Primary developer Chris Gorgolewski at Stanford.)
- Pycortex - Python tools for surface visualization. (Primarly developed by James Gao in the Gallant Lab at Berkeley)
- 3DSlicer - Open source medical imaging file processing and visualization tool.
- MRIConvert - Powerful file format converter.
- Horos (Mac) - Excellent DICOM visualization and sorting tool based off the commercial OsiriX viewer.
- Mango - Medical image viewer with analysis tools.
- FSL View - The viewer part of the FSL package that can also be used as a general viewer.
- BROCCOLI - A set of pre-processing and analysis routines that are optimized for GPUs.
- Human Connectome Project Workbench - A new and powerful set of visualization and data exploration tools from the HCP. (Although installation of the package is reportedly currently difficult.)
- GLM Denoise - A package for denoising task based fMRI data from Kendrick Kay.
- preprocessfmri - Kendrick Kay's powerful fMRI preprocessing script. Particularly useful if fieldmap corrections are being performed.
- Yeatman Lab Tools - Jason Yeatman's lab at the Univ. of Washington has a number of useful tools for MRI.
- CoAxLab Tools - Software and tools from the Cognitive Axon Lab at Carnegie Mellon.
- Surf Ice - Software for visualizing many types of fMRI data.
Other Useful General Software
- Cyberduck (Mac) - Good SFTP GUI.
- Atom - Excellent text editor that is well integrated with GitHub.
- Git/GitHub - The standard for version tracking code (and other stuff) and making it publicly available.
- Slack - Very userful lab/workgroup message system.
- PathFinder (Mac) - Excellent Finder replacement for OSX (because Finder is terrible). It allows sorting by extension, tabs, two pane file browsers, all the things you need to efficiently do science.
For MVPA
- libsvm - The most popular support vector machine classifier.
- Surfing - A toolbox for surface based voxel selection.
- PyMVPA - Python package for MVPA.
- Neural Decoding Toolbox - Matlab toolbox for MVPA.
- SearchMight - Searchlight toolbox from Francisco Pereira.
- Princeton MVPA Toolbox - MVPA toolbox from Princeton.
- MVPA Meanderings - Very good blog on issues in MVPA.
- Some tutorials from Rochester
For BIDS Conversion
- BIDS Specification
- BIDS Citation Paper
- Useful Tutorial
- https://github.com/nipy/heudiconv - Going from DICOMS to BIDS datasets (with folder structure)
- https://github.com/cbedetti/Dcm2Bids - Going from DICOMS to BIDS datasets (with folder structure)
- https://github.com/jmtyszka/bidskit - Going from DICOMS to BIDS datasets (with folder structure)
- https://github.com/dangom/dac2bids - Going from DICOMS to BIDS datasets (with folder structure)
- https://github.com/jooh/Dcm2Bids - Going from DICOMS to BIDS datasets (with folder structure)
- https://github.com/suyashdb/hcp2bids - HCP to BIDS
- https://github.com/INCF/openfmri2bids - OpenfMRI to BIDS
- Caspers 2017 OHBM Slides - Julian Caspers, a neuroradiologist, provided a great set of guidelines at the 2017 Organization for Human Brain Mapping conference.
- Atlas of the Human Brain -- Mai, Paxinos, & Voss
- Talairach Atlas online
- Brain Explorer from Allen Brain Institute
- Whole Brain Atlas - Harvard MGH
- Brainmaps.org
- Digital Anatomist - Univ. of Washington
- BrainVoyager Brain Tutor
- Video of Unfixed Brain - A rare and important look at a post-mortem brain that has not yet been fixed, thus showing the compressibility of the brain and details of vasculature.
- Marian Diamond's full anatomy course - The legendary Berkeley anatomy course.