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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/