An automated toolbox for doing PPI is now available at:
http://martinos.org/~mclaren/ftp/Utilities_DGM/PPPI/
createVec.m and defContrasts.m are also required and can be found at:
http://martinos.org/~mclaren/ftp/Utilities_DGM/
An example wrapper (looping through subjects and regions) and example input
structure (P) can be found at:
http://martinos.org/~mclaren/ftp/Utilities_DGM/example_structure_inputs/
The automated toolbox can do the following:
(a1) produce identical results to the current implementation in SPM
(a2) use the current implementation of PPI in SPM but using the regional
mean instead of the eigenvariate
(a3) uses a generalized form that allows a PPI for each task to be in the
same model using either the regional mean of eigenvariate
(b) creates the model using the output of one of the (a) options and the
first level design
(c) estimates the model (/results directory)
(d) computes the contrasts specified
To use the toolbox, you will need to change the following things in the
wrapper and input structure:
In the wrapper ppi_wrapper.m (in example_structure_inputs):
Change the following lines:
addpath('PPPIdirectory') --> replace PPPIdirectory with the location of the
PPPI directory that was downloaded
addpath('spm8directory') --> replace spm8directory with the location of spm8
(can be found by typing which spm)
Subjects={'subject1' 'subject2'}; --> put your subjects in '' inside the
{}.
regionfile={'region1.nii'...
'region2.nii'}; --> these are the VOIs files (.nii, .img, .mat) with full
paths to use for PPI, they are added to the input structure file by the
wrapper.
region={'region1'...
'region2'};--> these are the VOIs names, they are added to the input
structure file by the wrapper.
load('ppi_master_template.mat'); --> change if your calling the master
template something else.
save(['directory' region{regionnumber} '.mat'],'P'); --> change directory to
a location to save the inputstructure that has the region and VOI
information added to it.
Directory=['subjectdirectory']; --> change to location of 1st level
statistics. Can include variables (e.g. ['/Data/' Subjects{i} '/model/'])
load(['directory' region{regionnumber} '.mat']); --> should match the save
statement above.
save([Subjects{i} '_analysis_' region{regionnumber} '.mat'],'P');
PPPI([Subjects{i} '_analysis_' region{regionnumber} '.mat']); --> analysis
should be changed to something more identifiable (e.g. workingmemory_myname)
Now your set to run the wrapper. However, you need to modify the
master_template first for the options that you want to use. You should also
change the name in case others are also using it. In the case that you
change the name, it must also be changed in the wrapper above.
In the input structure fields of the template.mat file (in
example_structure_inputs):
These are set by the wrapper:
subject: the subject number, can also be the second argument of PPPI (set
in wrapper)
directory: either the first-level SPM.mat directory, or if you are only
estimating a PPI
model, then the first-level PPI directory (set in wrapper)
VOI: name of VOI file ('.nii', '.img', '.mat'). If you use a .mat
file, it should be 3 columns
containing the ijk voxel indices OR be a VOI.mat file from SPM.
(set in wrapper)
Region: name of output file(s), reqires two names for analysis (set in
wrapper) with two
VOI, regions should be separated by a space inside the ' '.
Output directory will
be Region. (if 2 regions, then the two regions will be
separated by a _ in the
directory name. (set in wrapper)
These should be set ahead of time.
contrast: contrast to adjust for. Adjustments remove the effect of the
null space of the
contrast. Set to 0 for no adjustment. Set to a number, if
you know the
contrast number. Set to a contrast name, if you know the
name. The default
is: 'Omnibus F-test for PPI Analyses'. If not set, reverts
to default setting.
analysis: specifies psychophysiological interaction
('psy'); physiophysiological
interaction ('phys'); or
psychophysiophysiological interactions ('psyphy').
extract: specifies the method of ROI extraction, eigenvariate ('eig') or
mean ('mean')
method: specifies traditional SPM PPI ('trad') or
generalized condition-specific PPI
('cond'). 'trad' is identical to SPMs current
implementation.
equalroi: specifies the ROIs must be the same size in all subjects
NOTE: default=1 (true); set to 0 to lift the
restriction. NOTE: that if your VOI
is outside of the 1L mask, it will return an error message
FLmask: specifies that the ROI should be restricted using the mask.img
from the 1L
statistics. NOTE: default=0. FLmask=1 does nothing if
equalroi=1.
VOI2: name of 2nd VOI for physiophysiological interactions
Weights: for traditional PPI, you must specify weight vector for each
task. Order
needs to be the same as Tasks below.
Tasks: In the generalized condition-specific PPI, you should specify
the tasks to
include in the analyses, but put a 0 or 1 in front of them
to specify if they must
exist in all sessions. NOTE: In traditional PPI, specify the
tasks that go with
the weights.
Estimate: specifies whether or not to estimate the PPI design. 1 means
to estimate
the design, 2 means to estimate the design from already
created
regressors (must be of the OUT structure), 0 means not
to estimate. Default
is set to 1, so it will estimate.
CompContrasts: 0 not to estimate any contrasts; 1 to estimate
contrasts; 2 to only
use PPI txt file for 1st level (not
recommended); 3 to only use PPI
txt file for 1st level and estimate contrasts
(not recommended); 2&3
are not recommended as they potentially do not
include all tasks
effects in the mode. Use at your own risk. 3
can not weight the
contrasts based on the number
of trials. Default is 0.
Contrasts: cell array of tasks to create contrasts to evaluate OR it is
a structure with
the following fields:
% left: tasks on left side of equation or 'none'
% right: tasks on right side of equation or 'none'
% Weighted: from Weighted below, default is 0; automatically
set from
Weighted
% STAT: 'T' or 'F'
% c: contrast vector from createVec, automatically generated
% name: name of contrast, will be defined if left blank
% Prefix: prefix to the task name (optional), can be used to
select each run
% Contrail: suffix after task name (e.g.
parametric modulators, different basis
function)
**If left blank and CompContrasts=1, then it defines
all possible T contrasts
for task components and across runs.
Weighted: Default is not to weight tasks by number of trials (0);
to change this,
specify which tasks should be weighted by trials. If
you want to weight
trials, then specify a duration longer than your
events. If you have a
mixed block event related design, then you can
average your events
based on number of trials and the blocks won't be
averaged IF Weighted
is set to be a number that is shorter than the block
duration and longer
than your events.
SPMver: SPM version used to create SPM.mat files at the first level.
maskdir: location to save seeds if VOI was a .mat file
** To set a field, type:
load template_master.mat
P.fieldname=value
save template_master.mat P
Please let me know if you run into any errors or have any questions.
Additionally, a paper describing the method should be available soon.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
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