AFNI program: 3dsvm
Output of -help
Program: 3dsvm
+++++++++++ 3dsvm: support vector machine analysis of brain data +++++++++++
3dsvm - temporally predictive modeling with the support vector machine
This program provides the ability to perform support vector machine
(SVM) learning on AFNI datasets using the SVM-light package (version 5)
developed by Thorsten Joachims (http://svmlight.joachims.org/).
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Usage:
------
3dsvm [options]
Examples:
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1. Training: basic options require a training run, category (class) labels
for each timepoint, and an output model. In general, it usually makes
sense to include a mask file to exclude at least non-brain voxels
3dsvm -trainvol run1+orig \
-trainlabels run1_categories.1D \
-mask mask+orig \
-model model_run1
2. Training: obtain model alphas (a_run1.1D) and
model weights (fim: run1_fim+orig)
3dsvm -alpha a_run1 \
-trainvol run1+orig \
-trainlabels run1_categories.1D \
-mask mask+orig \
-model model_run1
-bucket run1_fim
3. Training: exclude some time points using a censor file
3dsvm -alpha a_run1 \
-trainvol run1+orig \
-trainlabels run1_categories.1D \
-censor censor.1D \
-mask mask+orig \
-model model_run1
-bucket run1_fim
4. Training: control svm model complexity (C value)
3dsvm -c 100.0 \
-alpha a_run1 \
-trainvol run1+orig \
-trainlabels run1_categories.1D \
-censor censor.1D \
-mask mask+orig \
-model model_run1
-bucket run1_fim
5. Training: using a kernel
3dsvm -c 100.0 \
-kernel polynomial -d 2 \
-alpha a_run1 \
-trainvol run1+orig \
-trainlabels run1_categories.1D \
-censor censor.1D \
-mask mask+orig \
-model model_run1
6. Training: using regression
3dsvm -type regression \
-c 100.0 \
-e 0.001 \
-alpha a_run1 \
-trainvol run1+orig \
-trainlabels run1_categories.1D \
-censor censor.1D \
-mask mask+orig \
-model model_run1
7. Testing: basic options require a testing run, a model, and an output
predictions file
3dsvm -testvol run2+orig \
-model model_run1+orig \
-predictions pred2_model1
8. Testing: compare predictions with 'truth'
3dsvm -testvol run2+orig \
-model model_run1+orig \
-testlabels run2_categories.1D \
-predictions pred2_model1
9. Testing: use -classout to output integer thresholded class predictions
(rather than continuous valued output)
3dsvm -classout \
-testvol run2+orig \
-model model_run1+orig \
-testlabels run2_categories.1D \
-predictions pred2_model1
options:
--------
------------------- TRAINING OPTIONS -------------------------------------------
-type tname Specify tname:
classification [default]
regression
to select between classification or regression.
-trainvol trnname A 3D+t AFNI brik dataset to be used for training.
-mask mname Specify a mask dataset to only perform the analysis
on non-zero mask voxels.
++ If '-mask' is not used '-nomodelmask must be
specified.
For example, a mask of the whole brain can be
generated by using 3dAutomask, or more specific ROIs
could be generated with the Draw Dataset plugin or
converted from a thresholded functional dataset.
The mask is specified during training but is also
considered part of the model output and is
automatically applied to test data.
-nomodelmask Flag to enable the omission of a mask file. This is
required if '-mask' is not used.
-trainlabels lname lname = filename of class category .1D labels
corresponding to the stimulus paradigm for the
training data set. The number of labels in the
selected file must be equal to the number of
time points in the training dataset. The labels
must be arranged in a single column, and they can
be any of the following values:
0 - class 0
1 - class 1
n - class n (where n is a positive integer)
9999 - censor this point
See also -censor.
-censor cname Specify a .1D censor file that allows the user
to ignore certain samples in the training data.
To ignore a specific sample, put a 0 in the
row corresponding to the time sample - i.e., to
ignore sample t, place a 0 in row t of the file.
All samples that are to be included for training
must have a 1 in the corresponding row. If no
censor file is specified, all samples will be used
for training. Note the lname file specified by
trainlabels can also be used to censor time points
(see -trainlabels).
-kernel kfunc kfunc = string specifying type of kernel function:
linear : <u,v> [default]
polynomial : (s<u,v> + r)^d
rbf : radial basis function
exp(-gamma ||u-v||^2)
sigmoid : tanh(s <u,v> + r))
note: kernel parameters use SVM-light syntax:
-d int : d parameter in polyniomial kernel
3 [default]
-g float : gamma parameter in rbf kernel
1.0 [default]
-s float : s parameter in sigmoid/poly kernel
1.0 [default]
-r float : r parameter in sigmoid/poly kernel
1.0 [default]
-max_iterations int Specify the maximum number of iterations for the
optimization. 1 million [default].
-alpha aname Write the alphas to aname.1D
-wout Flag to output sum of weighted linear support
vectors to the bucket file. This is one means of
generating an "activation map" from linear kernel
SVMs see (LaConte et al., 2005). NOTE: this is
currently not required since it is the only output
option.
-bucket bprefix Currently only outputs the sum of weighted linear
support vectors written out to a functional (fim)
brik file. This is one means of generating an
"activation map" from linear kernel SVMS
(see LaConte et al, 2005).
------------------- TRAINING AND TESTING MUST SPECIFY MODNAME ------------------
-model modname modname = basename for the model brik.
Training: modname is the basename for the output
brik containing the SVM model
3dsvm -trainvol run1+orig \
-trainlabels run1_categories.1D \
-mask mask+orig \
-model model_run1
Testing: modname is the name for the input brik
containing the SVM model.
3dsvm -testvol run2+orig \
-model model_run1+orig \
-predictions pred2_model1
-nomodelfile Flag to enable the omission of a model file. This is
required if '-model' is not used during training.
** Be careful, you might not be able to perform testing!
------------------- TESTING OPTIONS --------------------------------------------
-testvol tstname A 3D or 3D+t AFNI brik dataset to be used for testing.
A major assumption is that the training and testing
volumes are aligned, and that voxels are of same number,
volume, etc.
-predictions pname pname = basename for .1D prediction file(s).
Prediction files contain a single column, where each line
holds the predicted value for the corresponding volume in
the test dataset. By default, the predicted values take
on a continuous range; to output integer-valued class
decision values use the -classout flag.
For classification: Values below 0.5 correspond to
(class A) and values above 0.5 to (class B), where A < B.
For more than two classes a separate prediction file for
each possible pair of training classes and one additional
"overall" file containing the predicted (integer-valued)
class membership is generated.
For regression: Each value is the predicted parametric rate
for the corresponding volume in the test dataset.
-classout Flag to specify that pname files should be integer-
valued, corresponding to class category decisions.
-nopredcensored Do not write predicted values for censored time-points
to predictions file.
-nodetrend Flag to specify that pname files should NOT be
linearly detrended (detrending is performed by default).
** Set this options if you are using GLM beta maps as
input for example. Temporal detrending only
makes sense if you are using time-dependent
data (chronological order!) as input.
-nopredscale Do not scale predictions. If used, values below 0.0
correspond to (class A) and values above 0.0 to
(class B).
-testlabels tlname tlname = filename of 'true' class category .1D labels
for the test dataset. It is used to calculate the
prediction accuracy performance of SVM classification.
If this option is not specified, then performance
calculations are not made. Format is the same as
lname specified for -trainlabels.
-multiclass mctype mctype specifies the multiclass algorithm for
classification. Current implementations use 1-vs-1
two-class SVM models.
mctype must be one of the following:
DAG : Directed Acyclic Graph [default]
vote : Max Wins from votes of all 1-vs-1 models
see https://lacontelab.org/3dsvm.htm for details and
references.
------------------- INFORMATION OPTIONS ---------------------------------------
-help this help
-version print version history including rough description
of changes
-------------------- SVM-light learn help -----------------------------
SVM-light V5.00: Support Vector Machine, learning module 30.06.02stim
Copyright: Thorsten Joachims, thorsten@ls8.cs.uni-dortmund.de
This software is available for non-commercial use only. It must not
be modified and distributed without prior permission of the author.
The author is not responsible for implications from the use of this
software.
usage: svm_learn [options] example_file model_file
Arguments:
example_file-> file with training data
model_file -> file to store learned decision rule in
General options:
-? -> this help
-v [0..3] -> level (default 1)
Learning options:
-z {c,r,p} -> select between classification (c), regression (r),
and preference ranking (p) (default classification)
-c float -> C: trade-off between training error
and margin (default [avg. x*x]^-1)
-w [0..] -> epsilon width of tube for regression
(default 0.1)
-j float -> Cost: cost-factor, by which training errors on
positive examples outweigh errors on negative
examples (default 1) (see [4])
-b [0,1] -> use biased hyperplane (i.e. x*w+b>0) instead
of unbiased hyperplane (i.e. x*w>0) (default 1)
-i [0,1] -> remove inconsistent training examples
and retrain (default 0)
Performance estimation options:
-x [0,1] -> compute leave-one-out estimates (default 0)
(see [5])
-o ]0..2] -> value of rho for XiAlpha-estimator and for pruning
leave-one-out computation (default 1.0) (see [2])
-k [0..100] -> search depth for extended XiAlpha-estimator
(default 0)
Transduction options (see [3]):
-p [0..1] -> fraction of unlabeled examples to be classified
into the positive class (default is the ratio of
positive and negative examples in the training data)
Kernel options:
-t int -> type of kernel function:
0: linear (default)
1: polynomial (s a*b+c)^d
2: radial basis function exp(-gamma ||a-b||^2)
3: sigmoid tanh(s a*b + c)
4: user defined kernel from kernel.h
-d int -> parameter d in polynomial kernel
-g float -> parameter gamma in rbf kernel
-s float -> parameter s in sigmoid/poly kernel
-r float -> parameter c in sigmoid/poly kernel
-u string -> parameter of user defined kernel
Optimization options (see [1]):
-q [2..] -> maximum size of QP-subproblems (default 10)
-n [2..q] -> number of new variables entering the working set
in each iteration (default n = q). Set n<q to prevent
zig-zagging.
-m [5..] -> size of cache for kernel evaluations in MB (default 40)
The larger the faster...
-e float -> eps: Allow that error for termination criterion
[y [w*x+b] - 1] >= eps (default 0.001)
-h [5..] -> number of iterations a variable needs to be
optimal before considered for shrinking (default 100)
-f [0,1] -> do final optimality check for variables removed
by shrinking. Although this test is usually
positive, there is no guarantee that the optimum
was found if the test is omitted. (default 1)
Output options:
-l string -> file to write predicted labels of unlabeled
examples into after transductive learning
-a string -> write all alphas to this file after learning
(in the same order as in the training set)
More details in:
[1] T. Joachims, Making Large-Scale SVM Learning Practical. Advances in
Kernel Methods - Support Vector Learning, B. Schoelkopf and C. Burges and
A. Smola (ed.), MIT Press, 1999.
[2] T. Joachims, Estimating the Generalization performance of an SVM
Efficiently. International Conference on Machine Learning (ICML), 2000.
[3] T. Joachims, Transductive Inference for Text Classification using Support
Vector Machines. International Conference on Machine Learning (ICML),
1999.
[4] K. Morik, P. Brockhausen, and T. Joachims, Combining statistical learning
with a knowledge-based approach - A case study in intensive care
monitoring. International Conference on Machine Learning (ICML), 1999.
[5] T. Joachims, Learning to Classify Text Using Support Vector
Machines: Methods, Theory, and Algorithms. Dissertation, Kluwer,
2002.
-------------------- SVM-light classify help -----------------------------
SVM-light V5.00: Support Vector Machine, classification module 30.06.02
Copyright: Thorsten Joachims, thorsten@ls8.cs.uni-dortmund.de
This software is available for non-commercial use only. It must not
be modified and distributed without prior permission of the author.
The author is not responsible for implications from the use of this
software.
usage: svm_classify [options] example_file model_file output_file
options: -h -> this help
-v [0..3] -> verbosity level (default 2)
-f [0,1] -> 0: old output format of V1.0
-> 1: output the value of decision function (default)
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Significant programming contributions by:
Jeff W. Prescott, William A. Curtis, Ziad Saad, Rick Reynolds,
R. Cameron Craddock, Jonathan M. Lisinski, and Stephen M. LaConte
Original version written by JP and SL, August 2006
Released to general public, July 2007
Questions/Comments/Bugs - email slaconte@vtc.vt.edu
Reference:
LaConte, S., Strother, S., Cherkassky, V. and Hu, X. 2005. Support vector
machines for temporal classification of block design fMRI data.
NeuroImage, 26, 317-329.
Specific to real-time fMRI:
S. M. LaConte. (2011). Decoding fMRI brain states in real-time.
NeuroImage, 56:440-54.
S. M. LaConte, S. J. Peltier, and X. P. Hu. (2007). Real-time fMRI using
brain-state classification. Hum Brain Mapp, 208:1033–1044.
Please also consider to reference:
T. Joachims, Making Large-Scale SVM Learning Practical.
Advances in Kernel Methods - Support Vector Learning,
B. Schoelkopf and C. Burges and A. Smola (ed.), MIT Press, 1999.
RW Cox. AFNI: Software for analysis and visualization of
functional magnetic resonance neuroimages.
Computers and Biomedical Research, 29:162-173, 1996.
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