Hi Nick,
I think that you have to define 2 regions of interest, like here:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;Vh5pnQ;20100215192827%2B0000
where one will refer to the SPM.mat and the other to the sphere.
The SPM index to provide for the nearest local maximum is the index in
the list of 'Regions of Interest' that correspond to the SPM considered.
Then the 'Expression' can be 'i2' or 'i1 & i2' whether you want all
voxels within the sphere or only those that are also above the threshold
in the SPM.
Best regards,
Guillaume.
Nicholas DiQuattro wrote:
> Hello,
>
> I'm trying to use the new VOI batch system to extract a region using the
> nearest local maxima option, but I am running into trouble with the
> required "SPM Index" Variable. If I define it to "1" it says "The SPM
> index does not correspond to a Tresholded SPM ROI." any higher numbers
> results in a "Index exceeds matrix dimensions."
>
> If someone could tell me what SPM index is referring to, or what I
> should set it to, I would appreciate it!
>
> thanks for your help,
> nick
>
> On Wed, Mar 24, 2010 at 9:20 AM, Guillaume Flandin
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Dear Mante,
>
> I'm sure there are scripts and toolboxes that would allow you to do so
> but, if you are using the latest version of SPM8, you can try to do
> something similar but simpler than what I described here:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;Vh5pnQ;20100215192827%2B0000
> i.e. set up a Volume of Interest module so that:
> * Select SPM.mat
> * Adjust data: index of the F-contrast to adjust for
> * Which session: index of session considered
> * Name of VOI: VOIname
> * Regions of Interest (1):
> * Sphere:
> - Centre: [12 17 -10]
> - Radius: 10
> - Movement of centre: Fixed
> * Expression: i1
>
> Best regards,
> Guillaume.
>
>
> Mante Nieuwland wrote:
> > Dear experts,
> >
> > I am trying to extract VOI time-series, but SPM seems to only want
> to do
> > this for supra-threshold voxels. So if the VOI is not
> supra-threshold for
> > specific subjects, SPM takes the nearest voxel (which might be way
> off). I
> > can adjust the threshold to be able to ´see´ and use the VOI, but
> I was
> > wondering whether maybe I am doing something wrong, or is there
> perhaps
> > another way to work around this issue? (or should I not be using
> those VOI
> > anyway?)
> >
> > I look forward to any responses, thank you very much in advance!
> > Mante
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
>
>
>
> --
> Nicholas DiQuattro
> Junior Specialist
> Integrated Attention Lab
> Center for Mind and Brain
> 267 Cousteau Place Davis, CA 95618
> tel: (530) 297-4472
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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