[VoxBo] vbdumpstats broken

[Stacy Huffstetler]

Sorry to repeat myself, but I'm still confused about what exactly mean
scaling and detrending refer to in the prm file.
What do those option do?  How do they apply to the data?  And how is it
possible to turn them on or off post-running the GLM?

Thank you very much,
Stacy

On 9/1/06, Evan Chen <echen2 at mail.med.upenn.edu> wrote:
>
> Hello Geoff,
>
> I think this may be related to my vbdumpstats question from a few days
> ago.
> In my case, the mean scaling and detrending options were somehow inserted
> multiple times (as both on and off) in the .prm file, resulting in
> vbdumpstats confusion.  Deleting the appropriate lines gave more
> appropriate
> results.  Beyond that, Dan has indicated that he is taking a closer look
> at
> the code for the cause of this issue and I'm including a portion of the
> correspondence below.  I hope this is helpful.
>
> Best,
> Evan
>
> >>>> Evan Chen wrote:
> >>>> contrast=mycontrast scale=t effdf=13.00 stat=2804.147468434274
> >>>> one-tailed_p=0.0000 two-tailed_p=0.0000
> >>> ...
> >> Thanks a lot for your suggestions!  Sadly, neither defining a
> contrasts.txt
> >> file nor setting the contrast flag to "foo t vec 1" worked and both
> produced
> >> the same t-value of 2804.  I did run the same ROI and contrast in IDL
> and
> >> got a much more reasonable result:
> >>
> >> Contrast: 1.0     * Effect
> >> t:       -3.7184586
> >> effdf:        13.000000
> >> p(one tail):       0.99871113
> >>
> >> Is there something simple that I could be missing here?
> >
> > For some reason, your parameter file has multiple lines indicating
> > whether or not it's mean scaled and/or detrended.  The first such
> > lines indicate that it is (both) and the second such lines indicate
> > that it isn't.  Here are the lines I mean:
> >
> > DataScale:     mean
> > Option: detrend
> > ...
> > DataScale:      none
> > Option: none
> >
> > The second is what you want for this kind of group (second tier)
> > analysis.  From the script file, it looks like you had the GLM set up
> > correctly, so I will have to take a look at the code and see how the
> > file got that way.  Apparently vbdumpstats believes the first such
> > lines, while the IDL voxel surfer believes the last.  Or something
> > along those lines.  You can get vbdumpstats to do the right thing by
> > editing the file to remove the first two lines, leaving intact the
> > "none" lines.  Once you do that, it produces the same results as IDL
> > (at least for the example you gave).  I will take a closer look at the
> > code to see how things got this way, and to make sure it isn't causing
> > other problems.
> >
> > dan
>
>
>
> On 8/31/06 2:43 PM, "Geoffrey K Aguirre" <aguirreg at mail.med.upenn.edu>
> wrote:
>
> > Dear Voxars ---
> >
> > The vbdumpstats command line routine has a bug. It does not respect
> > the settings in the .glm file regarding application of mean centering
> > and drift correction, and defaults to "on". As a consequence, the
> > values returned for group (random effects) analyses are messed up.
> >
> > Any help would be appreciated,
> >
> > Geoff
> >
>
> --
> Evan Chen, PhD
>
> Post Doctoral Research Fellow
> University of Pennsylvania
> 3 West Gates Building
> 3400 Spruce Street
> Philadelphia, PA 19104-4283
>
> echen2 at mail.med.upenn.edu
> Office: 215-614-0177
>
>
>
>
>


-- 
Stacy Huffstetler
Research Assistant
University of Pennsylvania
Center for Cognitive Neuroscience
Dr. Matthew Botvinick's Lab
Phone:  215-898-2966
http://ccn.upenn.edu/~mmb
shuffste at mail.med.upenn.edu
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