Dear SPM experts,
I try to write a batch script for PPI analysis of our fMRI data. There is an area defined by the results of the group level statistics (saved as an image). I would like to extract eigenvariates from this volume in an individual subject and to see the interactions with a block condition.
I the ppi_spm_batch written by Guillaume Flandin & Darren Gitelman the following lines are used for the extraction:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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);
...
While I need to use our mask instead of a sphere, but, unfortunately, I do not know how to do it. It is easy to perform in GUI mode, but not clear how to do it with the help of a batch. I prefer the latter in order to facilitate further data processing in multiple subjects.
Thank you a lot for your help!
Sincerely yours,
Vladimir
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