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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