%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
6/9/2001. See end of file for history.
Spatiotemporal and Weak Model ICA
---------------------------------
Jim Stone, John Porrill and Neil Porter,
Psychology Department, Sheffield University, UK.
Contents
--------
Overview of Program
Unpacking the STICA Tar File
Computational Requirements
Running Program Demonstration
Summary of Parameters
User Guide
Example Output
Copyright
Contact Information.
Acknowledgements
Overview of Program
-------------------
Independent component analysis (ICA) is a method for decomposing
mixtures of source signals into statistically independent signals
(ICs). It can be used for spatial and temporal signals, and has been
applied to EEG/ERP cite and fMRI data. An introduction to ICA can be
found at http://www.cnl.salk.edu/~tewon/ICA/preface.html.
This program implements algorithms presented in a tehnical report,
"Regularisation Using Spatiotemporal Independence and Predictability",
(JV Stone and J Porrill, Computational Neuroscience Technical Report
number 1, Psychology Department, Sheffield University). This can be
obtained from http://www.shef.ac.uk/~pc1jvs.
The code included in this program is written in MatLab (version
5.2.1), and tested on a Macintosh, Unix and PC.
The program is set up to process sequences of 2D images (e.g. fMRI
data), but could be adapted for other data. The program can be run in
several modes:
Spatial ICA: This decomposes an image sequence into a set of spatially
independent images and a corresponding set of dual temporal signals
(see cite Mck).
Temporal ICA: This decomposes an image sequence into a set of
temporally independent time courses and a corresponding set of dual
spatial images.
Spatiotemporal ICA: This decomposes an image sequence into a set of
spatial images and a corresponding set of time courses such that
signals in both sets are maximally independent.
Weak Model ICA: This regularises solutions found by ICA. The form of
weak model used here assumes that underlying sources signals or their
dual signals vary smoothly over time. This can be shown to improve the
nature of solutions found by ICA.
Skew_ICA: Use skew pdf, appropriate for images.
Note: This package is intended for people who want to see a quick
demonstration of ICA-related techniques, and for those who want to
adapt the code for their own uses. Programs with a more tutorial style
can be obtained via the web address given above.
Unpacking the STICA Tar File
----------------------------
The compressed tar file is called STICA_skew_demo.tar.
It can be unpacked on a unix machine using the command:
tar -xvf STICA_skew_demo.tar
This process creates a new directory STICA_skew_demo which contains the
following files directories:
README.txt - This file.
STICA - Top level directory.
STICA_CORE - Main code.
STICA_UTIL - Utilities.
STICA_CONJ_GRAD - Conjugate gradient optimisation.
STICA_FIND_VU_FAST - Weak model code.
STICA_NIPS_ADDD_ONS - Skew pdf code.
Computational Requirements
--------------------------
The code included in this program is written in MatLab (version 5.2).
Demonstration Program
---------------------
Set current directory to STICA_demo and then ensure that matlab can
access the required files by running typing:
jsetpath;
This adds three direectories to the current path.
The demonstration program demonstration can then be run by typing:
stica_demo;
to the matlab command line (stica_demo is in STICA_CORE).
The program makes synthetic fMRI data, and then
applies skew spatiotemporal ICA to it.
All of the code required to run the demonstration is in three directories.
Try setting the mode parameter to 's' (spatial ICA) then 't' (temporal
ICA) then 'st' (spatiotemporal ICA).
Only spatiotemporal ICA with skew spatial pdf model ('st' with SKEW_PDF_s=1)
recovers the original source signals.
Summary of Parameters
---------------------
The following parameters can be set from the file ica_demo.m.
--------------------------------------------------------------
Variable Type Description
--------------------------------------------------------------
RAND_SEED [int] Random number seed.
mode ['s','t','st'] ICA: spatial, temporal or spatiotemporal.
alpha [real] Ratio of spatial to temporal independence for stICA.
wm_sm [0,1] Add temporal smoothing weak model to sICA, tICA, or stICA.
beta [real] Ratio of [spatial,temporal] independence for weak model.
plot_inverval [int] Number of function evalutions between plotting results.
SKEW_PDF_s [0,1] Use skew pdf for spatial model (if set, ignore hi_kurt_s & lo_kurt_s)
SKEW_PDF_t [0,1] Use skew pdf for temporal model (if set, ignore hi_kurt_t & lo_kurt_t)
s_kurtosis ['hi','lo'] Kurtosis of spatial ICs - used with sICA and stICA.
t_kurtosis ['hi','lo'] Kurtosis of temporal ICs - used with tICA and stICA.
s_hi_kurt [0,1] Specify kurtosis of indvidual ICs (overrides s_kurtosis).
t_hi_kurt [0,1] Specify kurtosis of indvidual ICs (overrides t_kurtosis).
neig [int] Number of eigenvectors to use as input to ICA.
X [3D matrix] Input data: matrix of image sequences, used to obtain P and Q.
P [2D matrix] Matrix of neig temporal eigenvectors.
Q [2D matrix] Matrix of neig spatial eigenvectors.
W0 [2D matrix] Intiial (neig x neig) unmixing matrix.
W1 [2D matrix] Final (neig x neig) unmixing matrix.
S1 [2D matrix] Matrix of spatial signals found by ICA.
T1 [2D matrix] Matrix of temporal signals found by ICA.
%---------------------------------------------------------------------------------------
User Guide
----------
The program output is demonstrated below. The optimisation routine
prints various parameters, of which only f and |g| are of interest
here. f is the value of the function being minimised (estimated
negative of entropy of recovered ICs) , and |g| is the magnitude of
its gradient.
Example Output
--------------
In its current state the program's text output should appear as follows
on an SGI Indy R4400:
>> stica_demo
SETTING RANDOM NUMBER SEEDS TO 111
Using SPATIOTEMPORAL_ICA
pcs(:,1): jsize = 1600 1
Figures 1 and 2 are spatial and temporal eigenvectors.
pct: jsize = 1600 4
P: jsize = 1600 4
Q: jsize = 1600 4
stica: V0: jsize = 4 4
stica: d0: jsize = 1 4
THIS IS CONJGRAD ...
n= 1 |rho= 1.262030 lambda= 0.500000 | f= 13.8257 | |g|= 1.71974 step_len= 0.0576317
n= 11 |rho= 0.948245 lambda= 0.003906 | f= 5.86142 | |g|= 0.0472978 step_len= 0.441126
n= 21 |rho= 0.710472 lambda= 0.000015 | f= 5.77516 | |g|= 0.00875179 step_len= 0.142077
n= 31 |rho= 0.539425 lambda= 0.000000 | f= 5.76549 | |g|= 0.00308112 step_len= 0.088801
... stica done.
Elapsed time = 40.6 secs.
Copyright
---------
No part of this program should be used in any commercial application.
Acknowledgement of use by others should cite the technical report
associated with this software (i.e. "Regularisation Using
Spatiotemporal Independence and Predictability", by JV Stone and J
Porrill, Computational Neuroscience Technical Report number 1
Psychology Department, Sheffield University.).
Contact information
-------------------
,----------------------------------------------------------------------.
| Jim Stone, Wellcome Research Fellow, Sheffield University |
+----------------------------------------------------------------------+
| Psychology Department, | Email: j.v.stone@sheffield.ac.uk |
| Sheffield University | Tel (direct): +44 114 222 6522 |
| Sheffield, S10 2UR, | Fax: +44 114 276 6515 |
| England. | http://www.shef.ac.uk/~pc1jvs/ |
`-----------------------------------------------------------------------'
Acknowledgements
----------------
JV Stone is supported by the Wellcome Trust.
History
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盲源分离matlab代码.zip (510个子文件)
._STICA_CONJ_GRAD 82B
._STICA_CORE 82B
._STICA_FIND_VU_FAST 82B
._STICA_NIPS_ADDD_ONS 82B
._STICA_skew_demo 82B
._STICA_SKEW_README 539B
._STICA_UTIL 82B
._TEST_CONJ_GRAD 82B
._.DS_Store 82B
stica_demo.m 6KB
datat.m 6KB
sticafg.m 6KB
datat_skew.m 5KB
prepare_buchel_data.m 4KB
conjgrad_jvs.m 4KB
jrotate_surf_dots.m 4KB
jjrotate.m 3KB
jrotate.m 3KB
stica.m 3KB
ica_timax_init.m 2KB
jmake_stereoW.m 2KB
jmake_stereoW1.m 2KB
temp.m 2KB
file2var.m 2KB
basicfg_skew.m 2KB
basicfg_skew_ok.m 2KB
get_UxVx.m 2KB
datas.m 1KB
hplost.m 1KB
data_fmri.m 1KB
combin.m 1KB
spm_hrf.m 1KB
jset_color_defaults.m 1KB
wmfg.m 1KB
basicfg.m 1KB
go_timax_multvariate.m 1KB
pnshow.m 1KB
combrh.m 1KB
smooth_zs.m 1KB
make_spline_wrap.m 981B
jrandphase.m 950B
sticahist.m 941B
jshift_wrapR.m 907B
mv_svd.m 907B
jtest_jaffine.m 875B
get_VWDBsBt.m 843B
hplot.m 829B
plot_cross_section.m 821B
heval.m 805B
sicafg_porrill_orig.m 789B
sicafg.m 789B
mv_pca.m 751B
jgauss_wrap.m 729B
hplos.m 727B
gso_w.m 711B
gso.m 702B
hgrad.m 692B
show4sequences.m 669B
randk.m 660B
dprime.m 660B
jshift_region.m 655B
jshift.m 643B
get_VWDB.m 637B
zs2F.m 635B
findneig.m 621B
jaffinesolve.m 618B
randkm4.m 610B
stripmean.m 590B
jfig.m 590B
jmake_mask.m 582B
jconv_timax.m 577B
make_disc_noise_image.m 554B
get_VWD.m 547B
._stica_demo.m 539B
._sticafg.m 539B
._jsetpath.m 539B
checkgrd_stica.m 537B
jgauss.m 518B
mvs_stripmean.m 515B
make_disc_image.m 505B
jprint_mat_with_tabs.m 495B
mv_pca1.m 470B
find_nearpoint.m 463B
jprint_vec.m 462B
create_figures.m 437B
jmat_h_shift.m 424B
make_gauss2_mask.m 422B
jcorr_info.m 419B
jprint_mat.m 417B
jdetrend.m 400B
jsetpath.m 394B
jconvolve_old.m 392B
mv_stripmean.m 383B
main1.m 377B
jconvolve1.m 376B
spatial_freq2len.m 376B
jconvolve.m 374B
gradtest.m 371B
show4images.m 370B
jgauss2.m 368B
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