Title: The statistical analysis of fMRI data using FMRISTAT and MINC
1The statistical analysis of fMRI data using
FMRISTAT and MINC
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3PCA_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?
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5FMRIDESIGN example pain perception
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7FMRILM 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
81
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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10Results from 4 runs on the same subject
11MULTISTAT 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
12Target 100 effective df, so use 19mm smoothing
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14STAT_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
15STAT_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
16Estimating 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
17Shift of the hot stimulus
T stat for magnitude T stat for
shift
Shift (secs) Sd of shift
(secs)
18Shift 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
19Combining shifts of the hot stimulus (Contours
are T stat for magnitude gt 4)
20Shift of the hot stimulus
Shift (secs)
T stat for magnitude gt 4.93
21References
- 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.
22I/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
23Limitations 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
24Work-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
25A 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)?