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The statistical analysis of fMRI data using FMRISTAT and MINC

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Title: The statistical analysis of fMRI data using FMRISTAT and MINC


1
The statistical analysis of fMRI data using
FMRISTAT and MINC
2
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3
PCA_IMAGE PCA of time ? space
1 exclude first frames
2 drift
3 long-range correlation or anatomical effect
remove by converting to of brain
4 signal?
4
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5
FMRIDESIGN example pain perception
6
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7
FMRILM fits a linear model for fMRI time series
with AR(p) errors
  • Linear model
  • ?
    ?
  • Yt (stimulust HRF) b driftt c errort
  • AR(p) errors
  • ? ?
    ?
  • errort a1 errort-1 ap errort-p s WNt

unknown parameters
8
1
0.5
Hot - warm effect,
0
-0.5
-1
0.25
0.2
0.15
Sd of effect,
0.1
0.05
0
6
4
2
T effect / sd, 110 df
0
-2
-4
-6
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Results from 4 runs on the same subject
11
MULTISTAT mixed effects linear model for
combining effects from different
runs/sessions/subjects
  • Ei effect for run/session/subject i
  • Si standard error of effect
  • Mixed effects model
  • Ei covariatesi c Si WNiF ? WNiR

from FMRILM
?
?
Usually 1, but could add group, treatment,
age, sex, ...
Random effect, due to variability from run to run
Fixed effects error, due to variability within
the same run
12
Target 100 effective df, so use 19mm smoothing
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STAT_THRESHOLD thresholds and P-values
  • T, F, Hotellings T2, Roys maximum root (maximum
    canonical correlation)
  • Conjunctions of all these
  • Arbitrary number of dimensions (supply the
    resels)
  • Thresholds and P-values for
  • Local maxima (takes the best of Bonferroni,
    random field theory)
  • Cluster spatial extent (mm3 or resels) allowing
    for randomness in estimating local FWHM

15
STAT_SUMMARY SPM-style summary of local maxima
and clusters, and their P- and Q-values
  • Analyses T, F, Hotellings T2, Roys maximum root
    (maximum canonical correlation) volumes, and
    conjunctions of all these
  • Mask volume and mask threshold can be supplied
  • Supports isotropic (supply FWHM scalar) or
    non-isotropic (supply FWHM volume, from FMRILM or
    MULTISTAT) to calculate resels
  • Finds all local maxima and clusters above a
    threshold
  • Uses resels to calculate P- and Q-values for
  • Local maxima uses better of Bonferroni or random
    field theory
  • Clusters allows for randomness in estimating
    FWHM volume

16
Estimating the delay of the response
  • Delay or latency to the peak of the HRF is
    approximated by a linear combination of two
    optimally chosen basis functions

delay
basis1
basis2
HRF
shift
  • HRF(t shift) basis1(t) w1(shift)
    basis2(t) w2(shift)
  • Convolve bases with the stimulus, then add to
    the linear model

17
Shift of the hot stimulus
T stat for magnitude T stat for
shift
Shift (secs) Sd of shift
(secs)
18
Shift of the hot stimulus
T stat for magnitude T stat for
shift
Tgt4
T2
Shift (secs) Sd of shift
(secs)
1 sec
/- 0.5 sec
19
Combining shifts of the hot stimulus (Contours
are T stat for magnitude gt 4)
20
Shift of the hot stimulus
Shift (secs)
T stat for magnitude gt 4.93
21
References
  • http//www.math.mcgill.ca/keith/fmristat
  • Worsley et al. (2002). A general statistical
    analysis for fMRI data. NeuroImage, 151-15.
  • Liao et al. (2002). Estimating the delay of the
    response in fMRI data. NeuroImage, 16593-606.

22
I/O of MINC in FMRISTAT
  • I/O is written by Roger Gunn and John Aston,
    based on EMMA
  • dFMRIS_READ_IMAGE(file.mnc, slice, frame)
    reads minc file into MATLAB structure e.g.
    d.dim128 128 12, d.data array of data read
    in, etc.
  • FMRIS_WRITE_IMAGE(d, slice, frame) reverses this,
    supply d.file_name file_out.mnc and
    d.parent_file for like option of minc tools

23
Limitations of EMMA (1993)
  • EMMA flips an array if the step is negative, so
    voxel coordinates do not agree with e.g. register
  • Theres a lot of stuff in EMMA for PET data
    analysis that FMRISTAT never uses
  • EMMA limits the amount of data that can be I/O in
    one shot limit is now too low!
  • Can modify MINC file dimensions, but not step or
    start
  • EMMA cannot read vector data e.g. non-linear
    warps must use Louis def_to_vol to break up a
    vector into separate x, y, z volumes waste of
    space!
  • Some parts of EMMA use obsolete commands that do
    not exist in MATLAB 6.2, e.g. table
  • Need e.g. Frank to create a new EMMA for Windows
    with every new version of Windows or MATLAB

24
Work-arounds
  • Need to store 3 x 3 symmetric matrices at every
    voxel, so write them as 6 frames
  • Local FWHM volumes use 2 frames, 1 for local FWHM
    and 1 for local resels
  • PYTHON? Jonathan Taylor (Stanford) has translated
    FMRISTAT into PYTHON, and it can I/O MINC,
    ANALYZE and AFNI
  • FMRISTAT can I/O ANALYZE (not well tested) but
    not yet AFNI

25
A stat file type?
  • MULTISTAT takes as input, and produces as output
  • Effect volume
  • Sd volume
  • FWHM scalar or volume
  • DF scalar
  • Can we combine these into a single stat file
    using EMMA (or a replacement)?
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