Topics#

MR Basics#

  • MRI_magic: What is the measured signal

  • From signal to image

  • MR Glossary

Data Structure and Organization#

  • Dicom to Nifti

  • Interacting with neuroimaging data

  • BIDS

  • Defacing

Preprocessing#

  • Structural images

    • Intensity correction (bias (field) correction, inhomogeniety correction)

    • Brain extraction

      • Spatial Normalization

      • Segmentation and Parcellation

  • Functional images

    • Distortion correction

    • Motion estimates

    • Slice timing

    • Co-registration

    • Spatial normalization

    • Smoothing

  • How to do all of this: fmriprep

    • Steps it runs

    • Outputs

  • Quality control

    • MRI-QC: sMRI Quality Control

    • QC of fmriprep outputs

Data analysis#

  • Encoding

    • GLM

      • Design matrix

      • Convolution and filtering

      • How to deal with RT

  • Decoding (MVPA)

  • RSA

  • Intersubject synchronization

  • Latent state discovery

Visualization#

Data sharing/finding#

Getting help#

Resources#

https://dartbrains.org/content/intro.html
https://naturalistic-data.org/content/intro.html
https://mriquestions.com/
https://miykael.github.io/nipype_tutorial/
https://carpentries-incubator.github.io/SDC-BIDS-sMRI/
https://lukas-snoek.com/NI-edu/