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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

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 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

6 MRI signal Gradient field Summary of MRI 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 Metabolic pathway (local) Energy consumption LFP and BOLD

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) – 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 AxialCoronalSagittal

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

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

16 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

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 –

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