Example scripts for implementing batch mode analysis for a block design
with a few events thrown in
ts1 is the name of an experiment in which there were three different
task conditions and one rest condition.
The design was a block design.
Subjects participated in two runs each.
Each run had a fixed structure of alternation among the conditions, but
the order of runs was counterbalanced across subjects.
For more information on SPM batch mode, see spm_bch.man
get_ts1_sinfo.m: contains subject information,
including exam numbers, mappings of series numbers onto image types, i.e.
coplanar, epi, etc.
ts1_start.m: top-level script. This is the script
that is invoked from the matlab command line. It does the following things:
ts1_batch.m: top-level batch script. In this
script, the user selects which processing/analysis modules to run and which
subjects to run it on. This script then constructs the analysis queue structure
that SPM operates on.
Calls a routine (convert_format) which converts GE format data into Analyze
format (using slightly modified versions of Souheil's GE2SPM code) and
puts things into the correct directories (based on mappings in get_ts1_sinfo).
Note that my naming convention is slightly different from the one that
most other folks tend to use, and 'convert_format' may need to be modified
slightly to accomodate this difference.
Submits the batch script (ts1_batch) to the spm batch interface.
Scripts controlling individual components of the batch jobs:
ts1_defaults.m: sets various spm defaults
ts1_realign.m: creates structures containing
parameters for realignment, coregistration, and normalization. The
different realignment, coregistration, and normalization toggles in ts1_batch.m
(e.g. COREG_COPLANAR_2_HIRES) refer to different indices in the arrays
of realign, coreg, and normalize structures.
ts1_smooth.m: sets up structure that handles
smoothing of images. There are actually two structures. The
first handles smoothing of non-normalized resliced images, and the second
handles normalized images.
ts1_model_protos.m: Sets up a default
prototypical model structure for the experiment. This is where all
of the conditions, condition onsets, condition types, i.e. epoch or event,
convolutions, etc. are defined. Unlike the other batch modules which usually
have only a single structure associated with them, the model part of the
batch interface requires several structures.
Absolutely mandatory are:
Optional structures are
bf_ep -- for epoch (block) based design
bf_ev -- for events in design
For this particular experiment, the prototype corresponds to the model
that would be used for a subject whose run order was 1, 2. For subjects
receiving the blocks in reverse order, the conditions structure array indices
in the model structure would have to be switched. This is done dynamically
by ts1_model_norm.m, based on information in get_ts1_sinfo.m. Also, the
script contains specifications for two different types of models with different
numbers of conditions. The particular model to be used is selected through
the 'use_model_proto' global variable.
ts1_model_norm.m: Generates subject specific
models based on a desired prototype specified in ts1_model_protos.m.
Maps the appropriate files, etc. Also adds regressors (linear trend and/or
motion parameter estimates) if desired.
ts1_contrasts.m: This is where the contrast
structure is generated. This is done in two steps. First, all
of the desired contrasts are specified using my own scheme which is then
translated into the actual contrast structure. My scheme was developed
to use the names of conditions to dynamically generate the vectors of +1
-1 0, etc, rather than specifying the numbers directly. This makes
things much easier if you decide to change models by adding or deleting
a condition, because the same contrast will be generated even if the column
of a particular condition has changed. In its present implementation, this
scheme will not acccommodate contrasts such as -2 -1 +1 +2, etc.
Miscellaneous (non-spm-batch) scripts:
ts1_clean.m: Removes intermediate and rawdata
ts1_display.m: Invokes Matthew Brett's display_slices
routine to create various plots.
General utility scripts (not specific to this experiment)
convert_format.m: Converts GE data
to Analyze format using information in the get_*_sinfo.m file.
Things to watch out for ...
Global variables. There are a few global variables that are set in
various places that are required for the scripts to run properly.
All lower level scripts should execute independently. In fact, this
is a good way of debugging them before submitting them to the batch interface.
However, some of them rely on global variables that have been set in the
higher level scripts (usually *_batch.m and get_*_sinfo.m) for them to
run properly. If necessary, you can set a global variable in the
command window and then run your lower level script.
Some global variables are currently being used to handle situations
for which global variables are not the optimal way to do it. This
is most obvious when using the mutual information global flag. If
the flag is set true, mutual info is used for all coregistration, even
though this might not be the desired action. One way to get around
this might be to have coreg structures for mutual info coregistrations
defined in separate mfiles.
Debug your lower-level scripts by running them alone, i.e. invoke ts1_realign
and make sure it runs cleanly. Nothing bad will happen if you do
this and it will save you time in the long run. Debugging from within
spm batch mode is a pain in the ass.
Naming conventions for paths: The scripts assume a specific naming
of the directory tree.
In order to get the batch mode to work all the way, I had to modify
the following scripts from the SPM distribution. They must appear
on the Matlab path ahead of the SPM distribution.
I modified the bf_ev structure used for specifying event basis functions
in the model to return desired sets of gamma functions ('gamma_idxs' field).
I had to modify spm_get_bf.m to get this to work. Since this is a
"feature" rather than a "fix" I would rather not "contaminate/compromise"
the integrity of SPM99 by including it at this time. Please refer
to spm_bch.man for the official specification of the bf_ev structure.
These scripts (in particular the model and contrast sections) have been
debugged for a specific experiment and serve only as a model for customizing
scripts for your experiments. I make no claims that they will work
for you with little or no effort on your part.
Petr Janata <firstname.lastname@example.org>
Last modified: Fri Mar 16 23:29:09 2001