[VoxBo] HRF TR (sampling rate) - using default of 2000ms

[Daniel Y Kimberg]

Charan's answer was correct, but just to expand a bit:

Joonkoo Park wrote:
> That means if we are using a TR of 2000ms, using default HRF kernel should
> do fine, right?

Regardless of the TR of your data, you can use any HRF kernel you
believe to be a reasonable approximation of the HRF.  It's just
important that VoxBo knows the sampling interval of both your data and
the HRF estimate.  The stock HRFs we supply with VoxBo use the default
HRF interval of 2s.  If you use them, then you don't have to worry
about setting the sampling interval.  If you don't, and the interval
for your HRF estimates is not 2s, then you may want to use the -kr
flag, or specify it in the .glm file or in the glm interface.

Is it critical?  If the relationship between the two is off, then two
bad things can happen.  One, when you convolve your covariates, you're
going to have either a compressed or an expanded estimated response.
Two, if you choose to filter your data by (in part) convolving with an
HRF, your filter won't really be matched to your expected response --
you'll be getting either more or less temporal blurring than you
expect.  Temporal precision is much more important for event-related
than for blocked designs, but there's no reason not to get it right in
any case.  To help things along, you can add a line like the following
to your HRF file:

;TR(msecs): 3000

> Also, setting the HRF kernel by -kr flag is required only when you are using
> the stock HRF estimates that come with Voxbo (e.g.
> /usr/local/VoxBo/elements/noisemodels/smooth_params.ref), correct?

When you use the stock estimates, you don't need the flag, because
they use the default interval.  Incidentally, smooth_params.ref is a
1/f estimate, not an HRF estimate.  The HRF estimates are in the
neighboring filters directory, most people use Eigen1.ref.

vbmakeglm tells you the TR of the HRF and of your data, so it's
helpful to double-check it.  If you want to check a glm you've already
run, you can do:

vbmakeglm -v <glm dir>/*.glm

dan