Dear Alexa/List/Russ/Darren,

I'll have a look at your links, thanks. I have been thinking about these issues too. I adapted russ' code with the PSTH based on a FIR estimation somewhat, and incorparated it in our own PSTH-gui, where one can graphically select activation clusters on an anatomical overlay and calculate mean (over subjects) PSTHs over a cluster, by selecting group T-maps and single subjects' SPM.mat. 

This SPM-addon also allows one to interactively alter activation threshold, PSTH-Bin sizes and window, and correction options. One can now: 'not correct at all; correct for DCTs and intercept; correct for all events except those compared; correct for all events not in a particular PSTH (default PSTH in SPM)'.

I had some worries about correcting for all events not included in a particular PSTH. What users usually do is comparing for example the PSTH from event type A with B, and look at it's shape, amplitude, etc since it is considered 'real data' (...). However, when correcting the signal for all regressors in the model except the one you are plotting, one merely looks at the model for that regressor + noise , and hence this time plot is very much influenced by choices one makes for HRF, expected neural input function, etc. Let's say one models condition A,B,C,D and some nuisance regressors, I think it might be better to correct for C,D+nuisance regressors when for example plotting the PSTHs for condition A and B in one figure in order to conclude something from it. Than at least the modelling of B does not influence the PSTH for A and vice versa.

Are there any simulations on how robust PSTHs are for non-orthogonal regressors, i.e. influence of other events on your PSTHs? I think the best way is using M-sequences in your design when PSTH plots are important, but one does not always have this option.

Just some thoughts, correct me when I'm wrong.

I do some testing on how 'general' and bug-free our PSTH-tool is, and some time in the future I'll post it to the list to be subjected to your scrutiny.

Thank you very much for sharing your thoughts with me!

Bas

-------------------------------------------- 
Dr. S.F.W. Neggers 
dept. of Psychonomics,Helmholtz Institute 
Utrecht University 
Heidelberglaan 2 
3584 CS, Utrecht, room 17.09 
the Netherlands 
Tel: (+31) 30 253 4582 Fax: (+31) 30 2534511 
E-mail: [log in to unmask] 
Web: http://www.fss.uu.nl/psn/pionier 
-------------------------------------------- 



-----Oorspronkelijk bericht-----
Van: SPM (Statistical Parametric Mapping)
[mailto:[log in to unmask]]Namens Darren Gitelman
Verzonden: donderdag 12 augustus 2004 18:57
Aan: [log in to unmask]
Onderwerp: Re: [SPM] FW: [SPM] refs on PSTH


Alexa/List/Russ:

Thank you for this information.

Alexa, in relation to your question below my code allows the user to choose 
whether to adjust for various columns in the design matrix- essentially 
either for other sessions or for other events within the same sessions. I 
added this because we were trying to compare our results with results 
obtained from AFNI. To my understanding, which is based on a discussion 
with an AFNI user and not my direct first-hand experience, AFNI does not 
adjust for other events, but this could be incorrect. Answering, yes to 
both the adjustment questions will produce results as in SPM2 - spm_graph.

Cheers,
Darren


At 11:28 AM 8/12/2004, Alexa Morcom wrote:
>Hello list & Bas/ Russ
>
>It might be worth pointing out that although Russ's page is a good
>introduction to how these kinds of plots work, the PSTH plot works
>differently in SPM2 to SPM99, and it's the SPM99 method that Russ's page
>discusses. In SPM2, spm_graph fits an FIR model for the event of interest
>and it's this code that Darren & I have hacked.
>
>For more about the use of an FIR model to make inferences, see Rik Henson's
>HBM 2001 abstract at  http://www.fil.ion.ucl.ac.uk/~rhenson/refs.html. See
>also http://www.fil.ion.ucl.ac.uk/spm/data/ for Rik's sample datasets which
>include examples of the use of an FIR basis in the main model.
>
>Nobody's done anything formal to my knowledge on different ways of
>implementing code to make these FIR-PSTH plots, but the main decisions to
>make, as I undestand them, are a/ whether plots of more than one event type
>should deal with each separately and b/ whether one should adjust at the
>same time (or beforehand) for all other event types in the model. These are
>matters for individual choice but saying yes to a/ and b/ is to my mind the
>most consistent with spm_graph, and should mean that PSTH plots don't vary
>according to whether event type A is plotted against B or against C. With
>non-orthogonal regressors there are various ways that these choices can
>affect the results. I believe that Darren's program implements a choice
>about b/, but Darren please correct me if I'm wrong.
>
>I hope this helps!
>
>Alexa
>
>
>
>| -----Original Message-----
>| From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On
>| Behalf Of Russ Poldrack
>| Sent: 03 August 2004 16:25
>| To: [log in to unmask]
>| Subject: Re: [SPM] refs on PSTH
>|
>|
>| you can find a little more information here:
>|
>| http://sourceforge.net/docman/display_doc.php?docid=6217&group_id=13529
>|
>| the code in my roi toolbox (available at the same web site) implements
>| this kind of PSTH averaging based on an FIR model.
>|
>| cheers
>| russ
>|
>| On Aug 3, 2004, at 8:20 AM, Neggers, S.F.W. (Bas) wrote:
>|
>| > Dear SPMers,
>| >
>| > I'd like to read a little bit more about the theory behind extracting
>| > a PSTH from your data based on the estimates of a simple FIR model. I
>| > read through the code in spm_graph.m and get_psth.m from Darren, and I
>| > think I get the basic idea, but that's just not enough. Is there a
>| > more formal description of the PSTH approach followed in SPM, perhaps
>| > in the form of a paper doing some kind of validation?
>| >
>| > I plan to implement get_psth in an activation cluster based PSTH
>| > extractor, and really exactly like to know what I'm doing here.
>| >
>| > Kind regards,
>| >
>| > Bas
>| >
>| >
>| > --------------------------------------------
>| > Dr. S.F.W. Neggers
>| > dept. of Psychonomics,Helmholtz Institute
>| > Utrecht University
>| > Heidelberglaan 2
>| > 3584 CS, Utrecht, room 17.09
>| > the Netherlands
>| > Tel: (+31) 30 253 4582 Fax: (+31) 30 2534511
>| > E-mail: [log in to unmask]
>| > Web: http://www.fss.uu.nl/psn/pionier
>| > --------------------------------------------
>| >
>| >
>| ---
>| Russell A. Poldrack, Ph.D.
>| Assistant Professor of Psychology, UCLA
>| Franz  Hall, Box 951563
>| Los Angeles, CA 90095-1563
>| email: [log in to unmask]
>| phone: 310.794.1224
>| fax: 310.206.5895
>| web: http://www.poldracklab.org/
>|


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Darren R. Gitelman, M.D.
Cognitive Neurology and Alzheimer¹s Disease Center
Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
Voice:   (312) 908-9023     Fax:  (312) 908-8789
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