1. Research course on functional magnetic resonance imaging (non-invasive brain imaging)
Juha Salmitaival

2. Outline MRI safety course Introductory lectures (next week F227!)
Scanning (2 sessions for each participant)
Preprocessing
Data-analysis
Writing a research report
Note! You will not be able to plan and prepare the studies yourselves -> 5 cr

3. Today’s lecture Overview of the stages in an fMRI study MRI signal
BOLD hemodynamics & physiology
MRI protocol
Scanning settings
MRI images
Some artefacts
FSL introduction
Brain extraction
Introduction
-Cognitive Science & Neurobiology (not physics)

4. Stages of an fMRI study Research plan, funding
Ethical permission (HUCH) and research permission (AMI centre)
Setting up the experiment (stimulation, MRI protocol) and piloting
Collecting the data
Data-analysis
Preprocessing (motion correction, spatial/temporal filtering, brain extraction)
Data-analysis (model-based, e.g., GLM, data-driven, e.g., ICA, ISC)
Writing a manuscript

5. MRI signal T1 = realignment with the magnetic field
B0 field (e.g., 3T)
Larmor frequency
RF excitation / relaxation
T1 = realignment with the magnetic field
T2 = emission of energy
T2* = sensitive to inhomogeneties in the magnetic field
Relaxation is recorded with a head coil
Relaxation times are tissue specific

6. MRI signal Summary of MRI Gradient field MORE INFORMATION:
Gradient fields have three directions: slice selection, phase encoding, frequency encoding
Gradients change the precession frequency as a function of a location along the gradient axis
MORE INFORMATION:

7. BOLD hemodynamics BOLD (blood oxygenation dependent) signal
It takes about 4-6 seconds to reach its peak
HRF varies between subjects and brain region

8. BOLD physiology Neuronal activity Energy consumption LFP and BOLD
Metabolic pathway (local)

9. From neuronal activity to MRI signal

10. MRI protocol MRI sequence (RF excitation, gradient pulses)
Localizer, epi-sequence, anatomical sequence
TR (1.5 – 4 sec.), slice thickness (2-5 mm), number of slices (1-50), aquisition matrix (64 x 64 – 192 x 192), FOV, number of samples
Continuous imaging (jitter?) or sparse temporal sampling

11. Scanning ”settings” Fat suppression
Spectral spatial RF pulse minimum slice thickeness 3mm
Spectral RF (slice thickness < 3 mm)
Shimming (fMRI autoshim, DTI HOS - manual)
Optimizing the homogeneity of the B0 field
Correction of the inhomogeneity can also be done
Prescan (use auto prescan)
Optimal resonance frequency, adjusting transmit and receiver gain

12. MRI image Voxel (pixel in 3d) Volume (sample)
Slice thickness x FOV/matrix x FOV/matrix (in-plane resolution)
Volume (sample)
E.g., 30 x 64 x 64
4d image (typically > 100 MB, < 2 GB)
Formats: dicom, analyze, nifti, nifti gz

13. Anatomical and slice directions
Anatomical directions
Superior-inferior (head-foot)
Anterior-posterior (front-back)
Dorsal-ventral (back-front)
Right-left
Slice directions
Oblique planes can be scanned as well
Axial
Coronal
Sagittal

14. Artefacts (some of those)
Movement
Cross-talk
Aliasing
Chemical shift
Susceptibility artefact
Nyquist ghosting
Geometric distortion

15. Image preparation Dicom2nifti conversion (dcm2niigui) Image viewing
Output: FSL (4D NifTI) or Compressed FSL
Image viewing
Fslview (
MRIcron (
Data check
Orientation, artefacts

16. Toolbox selection Stimulus presentation Data-analysis
Presentation (nbs)
E-prime
Matlab
Data-analysis
FSL
SPM
Brain voyager
Freesurfer
AFNI
GIFT
Remember to add FSL to your bash

17. Homework - FSL Introduction
Website (
FSLUTILS
fslinfo
fslmaths
BET
FLIRT/FNIRT
FEAT
MELODIC

18. Brain extraction
Needed for image registration and artifact rejection

19. References & Images FSL-course SPM-course
SPM-course