same signal change values in two distinct regions

Hi,

I’m hoping some of the marsbar users can shed some light on a problem 
I’ve having.

I’ve recently created a series of ROI masks based on contrasts from 2 
experiments. Two of these masks consist of:

Con1 from Experiment 1 (p= 0.001) – Con1 from Experiment 2 (p=0.001)

Con1 from Experiment 2 (p= 0.001) – Con1 from Experiment 1 (p=0.001)

These create two distinct ROI masks in the parietal cortex (which don’t 
overlap).

When I run a batch script to look at % signal change from some of the 
conditions vs. baseline in Experiment I get identical values for these 
two ROIs (and different values for the other ROIs).

I thought this might be batch error but having done several checks using 
the GUI I’m getting the same thing, and the stats tables for these 
values are also identical. Also, when I use the GUI to view these ROI 
masks they are independent and in the regions I expect them to be in – 
so I don’t think anything is wrong with my ROIs

Is there a statistical reason why r1-r2 and r2-r1 should cause this to 
happen, or should I still be looking for an error?

Thank you in advance.

comparability of data from different scanning sessions

Dear MarsBaR experts,

I am a very new user of fMRI and are experiencing some unclarities 
concerning my data interpretation.
Our task required scanning the same subjects twice on two different days 
using the same task.
We conducted three conditions (A,B,C) on the first day and one condition 
(A2) on the second day.
A and A2 were basically the same. The scanner and scanning parameters 
were the same for the two days.

When extracting the time courses using MarsBaR, we experience the 
following strange phenomenon:

Conditions A,B,and C of the first day usually show similar time courses. 
However, compared to these
conditions, condition A2 stays always close to zero.

Hence, significant activations in a contrast A2 > B for instance, seem 
to be due to deactivation in B
rather than activation in A2. For the reverse contrast, B>A2, however, 
there seems to be activation
in B and no signal changes in A2.

This is the same for a large number of ROIs. The time course for the 
condition of the second day is
always close to zero with respect to the other conditions (although 
condition A2 of the second day
was identical to condition A of the first day).

Event-related FIR

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percent signal change for parametric modulations

Dear Matthew and other MarsBar experts,

I have posted the following email to the SPM mailing list last week, but
did not get a response. So since this is (indirectly) related to MarsBaR I
thought you could give me some comments ...

Thanks a lot for giving it some thought,
Jan

--- Forwarded Mail --------------------------------------------------------

Dear SPM experts,

I know, I know, percent signal change (psc) and how it is computed has been
discussed over and over on this list. However, here is another twist to it
and I wanted to get your opinion on it ...

Generally, one should compute a psc according to this recipe:
http://marsbar.sourceforge.net/faq.html#percent_signal

that is:
psc = (beta(task) * max(regr) * 100) / beta(constant)

where beta(task) is the effect of interest, max(regr) is the maximum of a
new convolved regressor, and beta(constant) is the session constant. The
newly convolved regressor contains only a single event with the duration of
the actual experiment and is convolved with the actual basis function
(which could be an HRF, but also one of the more complex basis sets).

However, when I have a parametric modulation as my effect of interest, then
the corresponding onset regressors models the average activation to all
events, and the parametric modulator models only the deviation of each
event from that average activation.

This implies, I *think*, that in order to get the correct psc one would
have to add the average activation on top of the effect of the modulator.
Or in an equation:

psc = ((beta(ons) + beta(pm)) * max(regr) * 100) / beta(constant)

where beta(ons) is the onset regressor that models the average activation,
beta(pm) is the beta of the parametric modulator and the rest is as above.

Does this all make sense?

Thanks,
Jan

--

-- 
Jan Gläscher, Ph.D.         Div. Humanities & Social Sciences
+1 (626) 395-3898 (office)  Caltech, Broad Center, M/C 114-96
+1 (626) 395-2000 (fax)     1200 California Blvd
glascher <at> hss.caltech.edu    Pasadena, CA 91125

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SPM5, Darw ROI

Hello Matthew and marsbar users,
                            I would like to draw anatomical ROI's and obtain FIR timecourse from the drawn regions. I could do this with
marsbar-0.38, but this feature dosen't seem to work with marsbar-0.41. Any help will be greatly appreciated.

Regards,

Binu

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QUESTION////////

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Fwd: QUESTION////////

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Re: QUESTION////////

Hi,

>         When I use Marsbar to generate an mask and then detect the average
> activity levels in the mask from a pic,I meet a problem.
>
>         We need to build a sphere, the point with the highest activity level
> in that region should be the centre of the circle ,and how can we find the
> highest-activity-level point with Marsbar?

You can't do that easily with Marsbar I'm afraid.  The usual procedure
is to find the point with highest activity from the SPM map, and use
that as the center in marsbar,

Best,

Matthew

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Question on FIR single and stacked

Dear Matthew and other Marsbarsians,

I'm trying to solve the question on wheter to use a single or stacked  
FIR to extract psth timecourses. I read all the posts of the  
mailinglist and the description in the "event_fitted_fir.m" but I'm  
not sure if I get the point...
If I'm interested in the timelocked signalcourse of a process, which  
lasts randomly between 9 - 12  seconds in each trial, do I have to  
choose stacked, or can I use single?

Thanks for any suggestions.

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conjunction analysis in marsbar

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