Research course on functional magnetic resonance imaging (non-invasive brain

imaging)

Juha Salmitaival

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

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

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

MRI signalB0 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

MRI signal

Gradient field Summary of MRI

MORE INFORMATION:http://www.cis.rit.edu/htbooks/mri/

BOLD hemodynamics

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

BOLD physiologyNeuronal activity

Metabolic pathway (local)

Energy consumption

LFP and BOLD

From neuronal activity to MRI signal

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

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

MRI image• Voxel (pixel in 3d)– 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

Anatomical and slice directions• Anatomical directions– Superior-inferior (head-foot)– Anterior-posterior (front-back)– Dorsal-ventral (back-front)– Right-left

• Slice directionsAxial Coronal Sagittal

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

Image preparation• Dicom2nifti conversion (dcm2niigui)– http://www.cabiatl.com/mricro/mricron/install.html – Output: FSL (4D NifTI) or Compressed FSL

• Image viewing– Fslview (

http://www.fmrib.ox.ac.uk/fsl/fslview/index.html)– MRIcron

(http://www.cabiatl.com/mricro/mricron/index.html)

– Data check• Orientation, artefacts

Toolbox selection• Stimulus presentation

– Presentation (nbs)– E-prime– Matlab

• Data-analysis– FSL– SPM– Brain voyager– Freesurfer– AFNI– GIFT

• Remember to add FSL to your bash

Homework - FSL Introduction• Website (www.fmrib.ox.ac.uk/fsl/fsl/list.html)• FSLUTILS– fslinfo– fslmaths

• BET• FLIRT/FNIRT• FEAT• MELODIC

Brain extraction• Needed for image registration and artifact rejection

References & Images

• FSL-course– http://www.fmrib.ox.ac.uk/fslcourse/

• SPM-course– http://www.fil.ion.ucl.ac.uk/spm/course/