[VoxBo] vbview bug report

[Daniel Y Kimberg]

Charan, thanks for the feedback.  I'd rather hear about these issues
this way than find out years later that everyone's been frustrated by
some really trivial bug (has happened a few times).  Here are some
thoughts:

> (1) We found that, once plotted, the fitted response for any covariate
> (or the overall fits) do not update when you change the voxel to be
> plotted. This initially gave me quite a scare.

Will make less scary.

> (2) I would like to be able to plot the fits on the same graph as the
> trial-averaged data. I thought I'd be able to do this by ctrl-clicking
> the plots of the trial average and the fits. Doing this leads the fit to
> be plotted, but the trial average is plotted as a straight line

I'll take a look at this, usually this means a scaling problem due to
a big difference in magnitudes, and sometimes you can fix it by
removing covariates of no interest (critically the intercept).  Other
times not.

> (3) I could not find how to change the scale (IRF-style vs. % change vs.
> % from zero, etc.)

Not totally available yet, I'll bump it up on the list.

> (4) I mentioned this before, but here it is again: once a GLM has been
> loaded, the program is unable to load a new GLM. Also, it fails to
> acknowledge changes to averages.txt after the GLM has been loaded (but
> before the time series panel has been opened).

Still not fixed, should be soon -- 1.8.3 was an emergency release, so
a lot of important stuff that wasn't quite ready didn't make it in.

> Other questions/comments:
> (*) The plotting of time courses for a masked region is excruciatingly
> slow. I'm not sure why this is the case for fairly small masks.

Yeah, I'm still playing with the code to do that efficiently.  It will
get a lot faster at some point, but I'll see if I can make it
moderately faster for now.

> (*) What is the use of the "interval" field in averages.txt? If your
> events are coded in TRs, it would seem that this field should be
> unnecessary.

Whether you're using TRs or time, you can ask it to over- or
under-sample your time series.  The default is 1 volume, but if you
want a different resolution, you can get it.  You also don't have to
start your trials on TR boundaries.

> (*) When coding the onset of events in terms of TRs, should we
> assume that the first event is "0" or "1"? (e.g., for an event
> occurring on the 20th TR, would we code that as 19 or 20?) This
> should be added to the documentation of the averages.txt file.

The first event is zero, the 20th TR is 19.  Will adjust help for
averages.txt (Dongbo, you can make this change in vbcfx as well once
I've committed my fix).

> (*) I'd like to see the "overlay" and "view GLM" options integrated if
> this is not a major pain.

Not sure what you mean by this -- do you just want to be able to surf
for any file to use as an overlay, and if you select a prm file it's a
GLM, otherwise it's an overlay?

> (*) I'd like to see the return of the handy "find region" and "find
> all" features.

You can do "find region at crosshairs," which is pretty close to the
former.  The region stuff is still pretty messy in vbview, but I'll
hack the "Find All Regions" button to also create a combined region
that includes everything.

> Finally a totally separate request:
> vbi does not seem to be able to read the origin from .img files (nifti
> format) that are produced by SPM. I also don't believe that the correct
> origin is imported by vb2tes. We can certainly manually set the origin,
> but will Voxbo be able to read the origin in the future?

That's weird, but there is at least one other serious bug in how we
process NIfTI files associated with SPM (try loading SPM5's
templates).  I'm going to take a look at that shortly.

dan