Dear Darren and others,
I have been succesfully using your function get_psth.m for a couple of studies now, using single session design. Works great. I made some minor (logistic) alterations and have also built a GUI around it allowing one to select ROIs and even calculate average PSTHs for selected events and models within these ROIs, and average over subjects. I'll share it on my sourceforge page as soon as I think it is ready and easy enough to use.
Currently I am analysing a 2 session design, and I ran into an error. The functions get_psth bails out at line 209 saying:
----
iu=find(SPM.Sess.U(events(n,n2)).u>0);
??? Field reference for multiple structure elements that is followed by more reference blocks is an error.
----
I had a look at the code, and I think I have found the error. The code around line 209:
202: for m = 1:length(sessions)
203: ses = sessions(m);
204:
205: xBF = SPM.xBF;
206: U = SPM.Sess(ses).U(ev(1));
207: % event vector in microtime, pool over columns in 'events'
208: for n2 = 1:size(events,2) %loop columns in 'events'
209: iu=find(SPM.Sess.U(events(n,n2)).u>0);
210: U.u(iu)=SPM.Sess.U(events(n,n2)).u(iu);
211: end
I suspect that one has to specify the session (variable 'ses' in the four loop) for which the 'find' function has to calculate the indices. This present code works for 1 session, but for more session the code tries to index a field directly at an array, which leads to the error.
I think that the correct code at line 209 should be:
209: iu=find(SPM.Sess(ses).U(events(n,n2)).u>0);
210: U.u(iu)=SPM.Sess(ses).U(events(n,n2)).u(iu);
Could you indicate whether this is OK? Perhaps I am not understanding the procedure well, and my patch leads to unwanted results....
The code now executes fine and I obtain a matrix with 2 columns in PSTH.events(..).psth, one column per session I think.
Is this correct?
Thank you in advance,
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/
>|
-------------------------------------------------------------------------
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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|
