Russ,
What constraints are on the event-related design? That is, why
would the program not return a blocked design (which is just a specific
case of an event-related design) as the most efficient
for a given minimal spacing between events (because without any other
constraints I am quite sure that this is the solution)? Just curious.
Sincerely,
Eric
>
> on the issue of determining an optimal trial ordering for an event-related
> design, Doug Greve at our center has a program (part of a larger suite of
> fmri analysis tools) that will iteratively search for the most efficient
> trial ordering and timing (based on a deconvolution model). Here is the
> info on how to download and install his package:
>
> ------------ Download --------------------
> Download the most recent version
> from ftp://ftp.nmr.mgh.harvard.edu/pub/flat/fmri-analysis
>
> % ftp ftp.nmr.mgh.harvard.edu
> user: anonymous
> passwd: your email
>
> ftp> cd pub/flat/fmri-analysis
>
> ftp> binary
> ftp> get fmri-YYMMDD.tar.gz
>
> Where YYMMDD corresponds to the most recent date.
>
> --------------- Install -------------------------
> Move fmri-YYMMDD.tar.gz to the directory under which you want
> the package to be installed. Delete or move any previous
> incarnations of the package.
>
> Uncompress the tar file:
>
> % gunzip fmri-YYMMDD.tar.gz
>
> This creates fmri-YYMMDD.tar which can be detarred:
>
> % tar xvf fmri-YYMMDD.tar
>
> This will create a directory called fmri-YYMMDD under which there
> are 4 subdirectories: bin docs src toolbox. You may want to
> create a symbolic link to fmri-YYMMDD from fmri:
> % ln -s fmri-YYMMDD fmri
>
> ---------------- Environment ----------------------------------------
>
> In your .cshrc file (or equivalent), create a new environment variable:
> setenv FMRI_ANALYSIS_DIR name-of-install-directory
>
> For those in the MGH-NMR center, you can set
> setenv FMRI_ANALYSIS_DIR /homes/nmrnew/home/inverse/fmri
>
> Add $FMRI_ANALYSIS_DIR/bin and $FMRI_ANALYSIS_DIR/bin/`uname -s`
> directories to your path.
>
> Add the toolbox directory to your matlab path. This is done
> by adding following lines to the startup.m file in your
> matlab directory (ie, ~/matlab/startup.m):
>
> fmri_analysis_dir = getenv('FMRI_ANALYSIS_DIR');
> fmritoolbox = sprintf('%s/toolbox',fmri_analysis_dir);
> path(path,fmritoolbox);
>
> Note that you must have matlab 5.2 or higher to run the software.
> The software has been tested under Linux, IRIX, and Sun. The scripts
> first look for a command called "matlab5" then for "matlab". If
> it does not find either of those, it will exit.
>
> To use the motion correction, you must have AFNI installed and its
> binaries in your path. For those in the MGH-NMR Center, you can
> add the following to your path:
>
> /space/beowulf/1/users/inverse/freesurfer_dist/bin/$os/afni
>
> where $os is the operating system (obtained from uname -s).
>
>
> ---------------- Getting Started ----------------------------------
>
> The file called overview.ps (or overview.tex) in the docs directory
> has information about what can be done with the software. There's
> also a lot more documentation as to how each program works.
>
> ---------------- Comments or Questions -----------------------------
> Send comments or questions to [log in to unmask]
>
> ---------------- Dislaimer ------------------------
> See docs/DISCLAIMER
>
> ---------------- Copywrite ------------------------
> See docs/COPYWRITE
>
>
>
>
> --
> Russell A. Poldrack, Ph. D.
> MGH-NMR Center
> Building 149, 13th St.
> Charlestown, MA 02129
>
> Phone: 617-726-4060
> FAX: 617-726-7422
> Email: [log in to unmask]
> Web Page: http://www.nmr.mgh.harvard.edu/~poldrack
>
>
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