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

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Presentation on theme: "Research course on functional magnetic resonance imaging (non-invasive brain imaging) Juha Salmitaival."— Presentation transcript:

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 (http://www.fmrib.ox.ac.uk/fsl/fslview/index.html) MRIcron (http://www.cabiatl.com/mricro/mricron/index.html) 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 (www.fmrib.ox.ac.uk/fsl/fsl/list.html) 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


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