You need to build a wrapper that creates all possible combinations of the three sets of par files.

Then use this to build a design matrix for each one.

Then estimate the efficiency (eff) and VRF (vrf) for the contrasts of interest.

M = C*inv(X'*X)*C';
eff = 1/trace(M);
vrf = 1/mean(diag(M));

Hope this helps.

Best Regards,

Donald McLaren, PhD

On Fri, Oct 16, 2015 at 1:34 PM, Sam Zorowitz <szorowi1@gmail.com> wrote:

Dear Freesurfer list,

Using the optseq2 program, is it possible to calculate the efficiency of a custom par file? I have an fMRI task that will be split into three blocks. I want to calculate the overall efficiency of my overall design byconcatenating the best par file from optimizing each individual block. I have already tried doing so by concatenating the three par files (updating the onset times) and inputting this into optseq2 by:

>> optseq2 --in new_file.par --nosearch --tr 1.75 --ntp 1080 --psdwin 0 3.5 1.75 --o new_dir

If I do this, however, I get a "core dump" error. Does anyone know how I might going about doing this? I've attached the new_par file for convenience.

Best,
sam

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