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SPM  September 2007

SPM September 2007

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Subject:

Re: Extracting event-locked averages from regions with no signal

From:

Volkmar Glauche <[log in to unmask]>

Reply-To:

Volkmar Glauche <[log in to unmask]>

Date:

Fri, 21 Sep 2007 12:49:29 +0200

Content-Type:

MULTIPART/MIXED

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (57 lines)

Dear Dani,

there were a number of posts quite recently about how to tweak SPMs 
masking. If you disable implicit (i.e. zero) masking and set the initial F 
threshold to 1 in defaults you should be able to estimate your model over 
your entire explicit mask. Otherwise, marsbar or Volumes toolbox may help 
to extract data.

Volkmar

On Thu, 20 Sep 2007, Daniel Simmonds wrote:

> Hello all,
>
>   We are currently conducting an fMRI study examining whether a novel
> pulse sequence will enhance signal in the OFC. In order to demonstrate
> the effectiveness of this method, wed like to graphically compare the
> raw time courses of the new vs. conventional sequences, and also compute
> and compare event-locked averages in the drop out regions (even though
> the signal in these regions will be a flat line). The main problem Im
> encountering with the latter is that during modeling, SPM eliminates
> regions where there is no signal, thereby precluding examination of
> event-locked averages in the drop out regions. Does anyone know how we
> could obtain raw time courses and event-locked averages for these
> regions? We are using SPM5 with Matlab 7.1.
>
>   Another separate issue is that our images contain portions of the
> skull and other external brain tissues. Weve tried to specify an
> explicit mask when creating single subject models to eliminate these
> regions (the mask.nii in the apriori folder), but these regions are
> still present after model estimation (i.e. SPM doesnt seem to
> acknowledge the mask, or does so very slightly). Weve also tried
> using the grey matter apriori for our explicit mask, which did not work
> either. Any suggestions? Thanks so much!
>
> Dani
>
>
> Daniel Simmonds
> Developmental Cognitive Neurology
> Kennedy Krieger Institute
> [log in to unmask]
>
>
>
> Disclaimer:
> The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
>

-- 
Volkmar Glauche
-
Department of Neurology		[log in to unmask]
Universitaetsklinikum Freiburg	Phone	49(0)761-270-5331
Breisacher Str. 64		Fax	49(0)761-270-5416
79106 Freiburg			http://fbi.uniklinik-freiburg.de/

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