This is one sub-module within the Neuroimaging cirriculum. Visit the link to view all the modules associated with the Neuroimaging Carpentries program.
fMRI Analysis in Python is a programme developed to facilitate reproducibility in functional neuroimaging analyses. Python is emerging as a standard language of data analysis, visualization, and workflow building. More recently, it has rapidly been adopted by the neuroimaging community as a means of developing powerful open-source tools in favour of historically used opaque software such as AFNI, FSL and SPM. In addition, the barrier to entry to Python is low - meaning that you as the user can easily develop your own packages and contribute to the open-source codebase of neuroimaging!
The fMRI Analysis in Python is a workshop series started up via a collaboration between researchers and staff at the Centre for Addiction and Mental Health (Toronto, ON), the University of Western Ontario (London, Ontario), and McGill University (Montreal, Quebec).
This lesson covers fMRI imaging analysis from the basic steps of preprocessing and data cleaning, to running an analysis, to exploring connectivity patterns in the brain.
| Time | Episode | Question(s) Answered |
|---|---|---|
| Setup | Download files required for the lesson | |
| 00:00 | 1. Exploring Preprocessed fMRI Data from fMRIPREP | How does fMRIPrep store preprocessed neuroimaging data. How do I access preprocessed neuroimaging data |
| 00:25 | 2. Introduction to Image Manipulation using Nilearn | How can we perform arithmetic operations on MR images |
| 01:10 | 3. Integrating Functional Data | How is fMRI data represented. How can we access fMRI data along spatial and temporal dimensions. How can we integrate fMRI and structural MRI together |
| 01:55 | 4. Preprocessing fMRI Data | What are the standard preprocessing steps? What existing pipelines help with preprocessing? |
| 02:25 | 5. Cleaning Confounders in your Data with Nilearn | How can we clean the data so that it more closely reflects BOLD instead of artifacts |
| 03:05 | 6. Applying Parcellations to Resting State Data | How can we reduce amount of noise-related variance in our data? How can we frame our data as a set of meaningful features? |
| 03:50 | 7. Functional Connectivity Analysis | How can we estimate brain functional connectivity patterns from resting state data? |
| 04:35 | 8. Neuroimaging Fundamentals & Nibabel | How are images loaded in Python? |
| 05:05 | 9. Introduction to Image Manipulation using Nilearn | How can be perform arithmetic operations on MR images |
| 05:50 | 10. Exploration of Open Neuroimaging Datasets in BIDS format | How does standardization of neuroimaging data ease the data exploration process |
| 06:35 | Finish |
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