AFNI & FMRI - the AFNI/NIfTI Server

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–23–Cartoon of Veins inside a VoxelDeoxyhemoglobinisparamagnetic(increases B)Rest of tissue+oxyhemoglobinis diamagnetic(decreases B)–24–BOLD Contrast• BOLD = Blood Oxygenation Level Dependent• Amount of deoxyhemoglobin in a voxel determines howinhomogeneous that voxel’s magnetic field is at the scaleof the blood vessels (and red blood cells)• Increase in oxyhemoglobin in veins after neuralactivation means magnetic field becomes more uniforminside voxel! So NMR signal goes up (T2 and T2* are larger), since itdoesn’t decay as much during data readout interval! So MR image is brighter during “activation” (a little)• Summary:! NMR signal increases 4-6 s after “activation”, due tohemodynamic (blood) response! Increase is same size as noise, so need lots of data
–25–• FMRI experiment designFMRI Experiment Design and Analysis! Event-related, block, hybrid event-block?! How many types of stimuli? How many of each type? Timing (intra- & inter-stim)?! Will experiment show what you are looking for? (Hint: bench tests)! How many subjects do you need? (Hint: the answer does not have 1 digit)• Time series data analysis (individual subjects)! Assembly of images into AFNI datasets; Visual & automated checks for bad data! Registration of time series images! Smoothing & masking of images; Baseline normalization; Censoring bad data! Catenation into one big dataset! Fit statistical model of stimulus timing+hemodynamic response to time series datao Fixed-shape or variable-shape response models! Segregation into differentially active blobso Thresholding on statistic + clustering and/or Anatomically-defined ROIanalysis! Visual examination of maps and fitted time series for validity and meaning• Group analysis (inter-subject)! Spatial normalization to Talairach-Tournoux atlas (or something like it)! Smoothing of fitted parameterso Automatic global smoothing + voxel-wise analysis or ROI averaging! ANOVA to combine and contrast activation magnitudes from the various subjects! Visual examination of results (usually followed by confusion)! Write paper, argue w/ mentor, submit paper, argue w/ referees, publish paper, …–26–FMRI Experiment Design - 1• Recall hemodynamic (FMRI) response! peak is 4-6 s after neural activation! width is 4-5 s for very brief (< 1 s) activation! $ two separate activations less than 12-15 s apart will have theirresponses overlap and add up (approximately — more on this in a later talk!)• Block design experiments: Extended activation, or multipleclosely-spaced (< 2-3 s) activations!Multiple FMRI responses overlap and add up to something moreimpressive than a single brief blip!But can’t distinguish distinct but closely-spaced activations; example:o Each brief activation is “subject sees a face for 1 s, presses button #1 ifmale, #2 if female” and faces come in every 2 s for a 20 s block, then 20 sof “rest”, then a new faces block, etc.o What to do about trials where the subject makes a mistake? These arepresumably neurally different than correct trials, but there is no way toseparate out the activations when the hemodynamics blurs so much in time.
Page 5 and 6: -9-Precession of Magnetization M•
Page 7 and 8: -13-Material Induced Inhomogeneitie
Page 11: -21-Neurophysiological Changes & FM
Page 16 and 17: -31-Fundamental AFNI Concepts• Ba
Page 18 and 19: -35-AFNI Dataset Files - II• AFNI
Page 20 and 21: -39-AFNI at the NIH Scanners• AFN
Page 22 and 23: -43-AFNI Time Series Graph ViewerDa
Page 24 and 25: -47-• Batch mode programsOther Pa
Page 26 and 27: -51-SUMA Teaser MovieColor from AFN

AFNI & FMRI - the AFNI/NIfTI Server

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