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What are some of the main points of Jenkinson and Chappel 2018: **Section 2.4** Functional MRI?
What are some of the main points of Jenkinson and Chappel 2018: **Section 3.4.1-3.4.8** Functional pipeline?
fMRI processing can be divided into two categories: preprocessing and analysis. How are they different?
What are some of the main points of [Esteban et al. 2019](https://d2l.arizona.edu/d2l/le/content/1094193/viewContent/13679729/View) ?
What are the advantages of fMRIprep over other fMRI processing tools?
How do you install fMRIprep?
When you run fMRIprep, what directories does it create?
How does fMRIprep encode versions?
What role does FreeSurfer play in fMRIprep?
What kind of distortion correction options are available in fMRIprep?
What is ICA Aroma in fMRIprep?
What are output spaces (for fMRIprep)?
What is an fMRIprep visual report?
How does one specify the task model for fMRI analysis?
What are some of the main points of [Botvinik-Nezer et al. 2020](https://d2l.arizona.edu/d2l/le/content/1094193/viewContent/12192747/View) ?
What are some of the main points of Jenkinson and Chappel 2018: **Section 3.4.9** Task fMRI statistical analysis?
What are some of the main points of Jenkinson and Chappel 2018: **Section 3.4.10** Resting state fMRI statistical analysis?
What are some of the main points of [Patterson et al. 2015](https://d2l.arizona.edu/d2l/le/content/1094193/viewContent/13936653/View) ?
What is the difference between GLM and ICA analysis of fMRI?
What is the fMRI concept "canonical HRF"?
What is Model Order Selection (ICA analysis)?
What are FNC and dFNC (fMRI analysis)?
What are some of the main points of Jenkinson and Chappel 2018: **Section 7** Surface-Based Analysis?
What are surface-based image formats?
What are the benefits of surface-based image formats?
What are some problems with surface-based formats?
What are some of the main points of Jenkinson and Chappel 2018: **Section 3.4.1-3.4.8** Functional pipeline?
(Student response here)
For me, the main point is the description of a typical preprocessing pipeline:
1) Distortion correction to fix the shape of each volume,
2) Motion correction (to compensate for motion between one volume and the next),
3) Slice-timing correction (to compensate for the time difference between the first and last slice of a volume),
4) Spatial smoothing (to improve signal-to-noise ratio),
5) Temporal filtering (to suppress frequencies that are not related to neural activity)
6) Intensity normalization (scaling the mean intensity to be consistent for a single subject, and later, during group analysis, scaling the mean intensity across subjects). Both choices facilitate statistics.
7) Registration (aligning the undistorted fMRI images to the T1w structural scan)
Do the different steps in the functional pipeline interact?
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