SPM Pre-Processing Talk Outline Talk Outline Henri Lartigue slit-scan photography

SPM Pre-Processing Talk Outline Talk Outline Henri Lartigue slit-scan photography www.phwiki.com

SPM Pre-Processing Talk Outline Talk Outline Henri Lartigue slit-scan photography

Ball, Jenn, Contributing Editor has reference to this Academic Journal, PHwiki organized this Journal SPM Pre-Processing Oli Gearing + Jack Kelly Methods as long as Dummies 07-04-2004 Talk Outline Slice Timing Realignment Coregistration Normalisation Smoothing Part 1 – Jack Part 2 – Oli Talk Outline Slice Timing Realignment Coregistration Normalisation Smoothing

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Henri Lartigue slit-scan photography exposed first exposed last slit-scan photography exposed first exposed last

slit-scan photography exposed first exposed last Slice Timing SPM assumes each scan is ‘instantaneous’ time in seconds 0 3 6 CORRECTED RAW TR TA Slice timing Only needed if: Temporal dynamics of evoked responses are important in addition to if TR is sufficiently small to permit interpolation ( <3 seconds ) BioPhysical latency is on the order of seconds Usually unnecessary if latency differences are modelled in SPM analysis “proper” using temporal derivatives. Slice timing Output: afilename.hdr afilename.img afilename.mat Talk Outline Slice Timing Realignment Coregistration Normalisation Smoothing Subject motion: front line defence Realignment of subject motion Why bother Subsequent analysis assumes that voxel = bit of brain (e.g. Subtraction in addition to averaging) haemodynamic response is small compared to signal from movement increase sensitivity of T-Test (movement contributes to variance) Realignment of subject motion When to do it Must be be as long as e Normalization Can be either be as long as e or after slice time correction (disadvantages to both options) For interleaved acquisitions it’s recommended to slice time correct first For sequential acquisitions it’s recommended to realign first Realignment of subject motion coregister filename.mat reslice filename.img rfilename.img Realignment Realignment involves: “coregister” - Estimate 6 parameters (3x translations, 3x rotations) of an affine rigid body trans as long as m. Aim: minimize COST FUNCTION computed between each successive scan in addition to a reference scan Realignment Realignment involves: 2. “reslice” Apply trans as long as mation by re-sampling the data fMRI adjustment In extreme cases, up to 90% of the variance in fMRI time-series can be accounted as long as by effects of movement AFTER realignment: subject movement between slice acquisition interpolation artefacts nonlinear distortion due to magnetic field inhomogeneities (EPI distortion) spin-excitation history (especially if TR approaches T1) fMRI adjustment Adjustment can be carried out as either: Part of the pre-processing step or Embodied in model estimation during the ‘real’ analysis. EPI undistortion EPI images are distorted relative to the structural scans Bigger magnet = more distortion EPI undistortion Different tissues have different magnetic susceptibilities Magnetic field warps at tissue boundaries But the field gradient encodes position! EPI undistortion It is possible to directly measure the magnetic field across the head, in addition to then use this in as long as mation to undistort the EPI images after reconstruction. EPI undistortion new feature in SPM2: Talk Outline Slice Timing Realignment Coregistration Normalisation Smoothing Ball, Jenn Angeleno Modern Luxury Contributing Editor www.phwiki.com

Coregistration Align different modalities (eg PET & MRI) Align functional (EPI) with structural (T1) Optimize parameters describing rigid body trans as long as mation to match functional with structural SPM99’s 3-step coregistration procedure is replaced by an “in as long as mation theoretic objective function” in SPM2 Part 2 Slice Timing Realignment Coregistration Normalisation Smoothing Part 1 – Jack Part 2 – Oli Normalisation in addition to smoothing The story so far fMRI time data set Movement between scans has been corrected as long as (realignment) Functional data has been overlaid onto the high resolution anatomical data (co-registration) What next

Talk Outline Slice Timing Realignment Coregistration Normalisation Smoothing Normalisation What do we want from fMRI Analysis within subject data Analysis between subjects But how do we compare 2 different brains Squash the subjects data into a common 3D brain space. The Talairach brain template1 1Talairach in addition to Tournoux, 1988

Summary Realignment – (adjust as long as movement between slices) Co-registration – (link functional scans to anatomical scan) Normalisation – (warp functional data into template space) Smoothing – (to increase signal to noise ratio) Any questions Ask Dan / Will / Lucy Resources SPM99 manual www.fil.ion.ucl.ac.uk/spm/course/manual/spatial.htm What’s new in SPM2 www.fil.ion.ucl.ac.uk/spm/spm2.html New Cambridge’s CBU imaging www.mrc-cbu.cam.ac.uk/Imaging/Common/fmridefaults.shtml General info (on everything) www.WikiPedia.org

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