fMRIPrep Overview

Parent item: Personal Work Notebook (https://www.notion.so/Personal-Work-Notebook-ec03daaf2ac048be88c6f12c933a3b16?pvs=21) Done: Done Doc Type: SOP/Doc Important Doc: No

Documentation Webpage:

https://fmriprep.org/en/stable/outputs.html 1

General Overview

*Diagram of fMRIPrep, 04-26-24* Dashes indicate optional data or processes. The “fit” derivatives include a collection of individual volumes and transform files. The “transform” section shows the process used to generate resampled BOLD series. The available inputs, such as fieldmaps and slice-timing metadata, and the target space, such as an MNI template, determine the final result.

Diagram of fMRIPrep, 04-26-24 Dashes indicate optional data or processes. The “fit” derivatives include a collection of individual volumes and transform files. The “transform” section shows the process used to generate resampled BOLD series. The available inputs, such as fieldmaps and slice-timing metadata, and the target space, such as an MNI template, determine the final result.

Step 1) Anatomical preprocessing

  • Brain Extraction
  • Brain tissue segmentation(making brain mask)
  • Spatial nomalization(e.g MNI152LinAsym:res-2)

Step 2) BOLD preprocessing

  • HMC(We use reference BOLD image gained from t1-saturated image)
  • STC
  • SDC
  • resampling BOLDs into native spaces(This part was very tricky for me. I understood this process as followings. 1. combine each transform matrix into one transform matrix 2. apply one transform matrix onto each volume images)
  • EPI to T1w registration (re-align EPI images onto normalized t1w)
  • finally, normalize EPI images onto standard image.

*Note: We try to resample as few times as possible. So while we do always resample to native (STC + HMC + SDC), that is used for processes that need data in native BOLD space. When we resample to T1w space, we apply (HMC + SDC + BOLD-to-T1w) in a single step from the STC’d (if applied) time series.