fMRI preprocessing

Specificities of preprocessing steps tend to vary across software. See packages for details:

• SPM
  • CONN
• AFNI
• FSL

General steps

1. Realignment → estimate and correct subject motion effects
2. Susceptibility distortion correction → estimate & correct spatial distortions due to inhomogeneities in the magnetic field
3. Slice timing correction → correct for temporal distortions due to intrinsic sequential nature of scanning acquisition protocol
4. Co-registration and normalization → align functional and anatomical data across different subjects

Correction of noise sources and signal confounds has a considerable impact on neuroimaging results Khalili-Mahani2013

Noise sources are exacerbated under Psychedelics → increase head motion during scanning and alter blood pressure, respiration, heart rate Griffiths201 Holze2021 Olbrich2021

global signal regression has been found to substantively alter psychedelic effects on resting-state measures Preller2020 Preller2018

Topics

SPM
FSL Tutorial
CONN Tutorial

Things to watch for

1. gibbs ringing artifacts
2. abnormal intensity differences in GM/WM indicative of pathology (here)