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Resources

This page provides links to written documentation, tutorials, and videos for relevent software in neuroimaging analysis.

Andy's Brain Book

Andy's Brain Book is an ongoing teaching effort by Dr. Andrew Jahn and is the sort-of successor to Andy's Brain Blog. For researchers new to fMRI analysis, this is a very useful breakdown of how to perform an analysis and interpret data with a variety of common software.

He also has video series going through different types of analyses himself.

Learning Neuroscience

A variety of message boards and mailing lists exist when searching for answers in neuroscience or in general. There are also various conferences and courses you can take to learn more about neuroimaging analysis. A list of some of the more helpful ones can be seen below:

  1. Neurostars: message board with a wide array of neuroscience topics.
  2. NITRC: focuses more on specific software and technical questions in neuroimaging
  3. Neurohackademy: A summer school in neuroimaging and data science at University of Washington. Also have recordings of courses from previous years covering a huge variety of topics in the computational space.
  4. Neuromatch: online community of computational neuroscientists whose mission is to foster inclusive global interactions for learning, mentorship, networking, and professional development. There is an academy that focuses on teaching students through small group projects and a conference that provides a virtual platform for sharing scientific ideas and research.
  5. A more complete list

Software

Most video links on the page will go to the MRI analysis playlist on UAB Research Computing's Youtube channel.

BIDS

  1. BIDS Specification Documentation
  2. BIDS Apps
  3. BIDS Workshop (UAB Feb 2022)
    1. Github Repo
    2. Presentation Recording

fmriprep

  1. Main fmriprep docs
  2. fmriprep Cheaha Video Tutorial

MRIQC

  1. Main MRIQC Docs
  2. MRIQC Cheaha Video Tutorial

QSIprep

  1. Main QSIprep Docs
  2. QSIprep Cheaha Video Tutorial

Data Repositories

Some projects may want to take advantage of published data. This is a short list of repositories for MRI data with different modalities and participant demographics. If you would like a repository added to this list, please submit an issue on our documentation's github page.

Human Connectome Project

  1. Young Adult Dataset
    1. Database site. Data collection has completed
    2. Demographics: >1000 Healthy participants aged 18-32
    3. Accessibility: Free account available to anyone associated with a university. No access renewal required
  2. Aging Dataset
    1. Database Site. Data collection is ongoing.
    2. Demographics: 1200 healthy participants aged 36-100+
    3. Accessibility: Access via NDAR account. Access must be renewed yearly
  3. Development Dataset
    1. Database Site. Data collection is ongoing.
    2. Demographics: 1350 healthy participants aged 5-21
    3. Accessibility: Access via NDAR account. Access must be renewed yearly

Adolescent Brain Cognitive Development

  1. Main site
  2. Database Site
  3. Demographics: 12,000 children originally aged 8-10. Longitudinal scans over 10 years.
  4. Accessibility: Access via NDAR account. Access must be renewed yearly

Alzheimers Disease Neuroimaging Initiative

  1. Main Site
  2. Demographics: >400 AD patients and controls. See exact breakdown across the multiple studies on their site
  3. Accessibility: See details

OpenfMRI

OpenfMRI is a data warehouse containing a large number of publicly available datasets. These data are distributed using a Pulic Domain license, and so no registration or license agreement is necessary for accessing these data. Data scope and type vary highly across submitted studies. These data can be useful for both analyis for the purpose of publishing as well as teaching and learning.