Using 1 should be fine, unless SPM12 has changed the check. The lines from spm_getSPM.m that checks this are (from a reasonably updated SPM8 release):
            try
                u = xSPM.u;
            catch
                u = spm_input(['threshold {',STAT,' or p value}'],'+0','r',0.001,1);
            end
            if u <= 1
                thresDesc = ['p<' num2str(u) ' (unc.)'];
                u = spm_u(u^(1/n),df,STAT);
            else
                thresDesc = [STAT '=' num2str(u) ];
            end
            
So as long as the threshold is less than or equal to 1 it is interpreted as a p-value.

-Mike

--
  Mike Angstadt
  Research Computer Specialist / PANLab Lab Manager
  Department of Psychiatry / University of Michigan
  (734) 936-8229

From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of MCLAREN, Donald
Sent: Wednesday, June 03, 2015 11:23 PM
To: [log in to unmask]
Subject: Re: [SPM] SPM PPI batch script question about VOI extraction

Franka,

First, I would suggest that you read my 2012 paper on generalized psychophysiological interactions for a discussion on how to best model the connectivity during different conditions. As you will see in the paper, the gPPI models are more accurate.

Second, the gPPI toolbox allows pre-specified ROIs will requiring any activation level. This is actually my preferred approach as I can be sure that all voxels in the ROI are used to compute the connectivity. The gPPI toolbox is automated given a parameter structure and first-level SPM.mat file.

As I wrote the gPPI toolbox, I haven't used the PPI scripts in SPM in several years. However, my recollection is that you can set P to .99999. Setting it to 1 I believe flips it to be interpreted as a test statistic.


Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Jun 1, 2015 at 12:56 PM, FR <[log in to unmask]> wrote:
Hi all,

I have been using the SPM batch script to do PPI analysis. At one point of the script I am not 100% sure what the script does, and I was hoping for some feedback. I have read a few related discussions, but I am still not 100%  I understand correctly.

The original script (http://www.fil.ion.ucl.ac.uk/spm/data/attention/ppi_spm5_batch.m) was used to analyse whether the connectivity between V2 and V5 in response to motion changes in conditions of attention and no attention.
For the purpose of this analysis it was therefore important to extract the time course from a region that showed significant motion activity.

If I understand the script correctly, therefore the analysis involves looking at the motion contrast, and extracting the timecourse from a coordinate that was significant in the motion contrast.

This is the section from the batch script:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% VOLUME OF INTERESTS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% EXTRACTING TIME SERIES: V2
%=====================================================================

% DISPLAY THE MOTION CONTRAST RESULTS
%---------------------------------------------------------------------
clear jobs
jobs{1}.stats{1}.results.spmmat = cellstr(fullfile(data_path,'GLM','SPM.mat'));
jobs{1}.stats{1}.results.conspec(1).titlestr = 'Extracting V2: Motion';
jobs{1}.stats{1}.results.conspec(1).contrasts = 3;
jobs{1}.stats{1}.results.conspec(1).threshdesc = 'FWE';
jobs{1}.stats{1}.results.conspec(1).thresh = 0.05;
jobs{1}.stats{1}.results.conspec(1).extent = 0;
jobs{1}.stats{1}.results.print = 0;
spm_jobman('run',jobs);

% EXTRACT THE EIGENVARIATE
%---------------------------------------------------------------------
xY.xyz  = spm_mip_ui('SetCoords',[15 -78 -9]);
xY.name = 'V2';
xY.Ic   = 1;
xY.Sess = 1;
xY.def  = 'sphere';
xY.spec = 6;
[Y,xY]  = spm_regions(xSPM,SPM,hReg,xY);


My question is slightly different. Rather than looking for a coordinate that showed a significant effect in my dataset I have a coordinate predefined from the literature.

I believe in order for the script to work, it is still necessary to display a contrast that is thresholded at some level, simply because the extraction of the eigenvariate requires the GUI interface.  For the purpose of my analysis, I would assume that I simply load any(?) contrast and set the p-value to 1 and the "extent" to 0, the goal being that for each participant the timecourse is extracted from the same, independently defined coordinate.
Here is my reasoning for this: If I understand correctly, which contrast I use does not matter, because I am extracting the time course for the entire session anyways, and as the P-value would be set to 1 it would get the time course from exactly the coordinate I specify. If this is in fact the case, I should get the same results for any contrast.

Can someone conform whether I understood this correctly, or clarify, if there is a misconception is what I have written?

Thanks a lot!

Franka

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