Summary of what happened:
I have ran the “default mni” preprocessing on my fMRI dataset and now I need to generate the connectivity maps. I am a bit confused about what to write on my batch script and which of the preprocessing outputs have to be the input for this analysis. Below is the script I have so far but not sure how to complete it:
Command used (and if a helper script was used, a link to the helper script or the command generated):
clear batch;
%fetching an existing conn project
batch.filename = 'filepath/Preprocessing.mat';
%CONN Setup
batch.setup.isnew = 0;
batch.Setup.nsubjects=NSUBJECTS;
batch.Setup.RT=TR;
%Here is Where I do not know what to specify
batch.Setup.functionals=repmat({{}},[NSUBJECTS,1]);
for nsub=1:NSUBJECTS,for nses=1:nsessions,batch.Setup.functionals{nsub}{nses}{1}=???; end; end
batch.Setup.structurals=???;
nconditions=nsessions; % treats each session as a different condition
if nconditions==1
batch.Setup.conditions.names={'rest'};
for ncond=1,for nsub=1:NSUBJECTS,for nses=1:nsessions, batch.Setup.conditions.onsets{ncond}{nsub}{nses}=0; batch.Setup.conditions.durations{ncond}{nsub}{nses}=inf;end;end;end % rest condition (all sessions)
else
batch.Setup.conditions.names=[{'rest'}, arrayfun(@(n)sprintf('Session%d',n),1:nconditions,'uni',0)];
for ncond=1,for nsub=1:NSUBJECTS,for nses=1:nsessions, batch.Setup.conditions.onsets{ncond}{nsub}{nses}=0; batch.Setup.conditions.durations{ncond}{nsub}{nses}=inf;end;end;end % rest condition (all sessions)
for ncond=1:nconditions,for nsub=1:NSUBJECTS,for nses=1:nsessions, batch.Setup.conditions.onsets{1+ncond}{nsub}{nses}=[];batch.Setup.conditions.durations{1+ncond}{nsub}{nses}=[]; end;end;end
for ncond=1:nconditions,for nsub=1:NSUBJECTS,for nses=ncond, batch.Setup.conditions.onsets{1+ncond}{nsub}{nses}=0; batch.Setup.conditions.durations{1+ncond}{nsub}{nses}=inf;end;end;end % session-specific conditions
end
batch.Analysis.name = 'SBC';
batch.Analysis.type = 2;
batch.Analysis.overwrite = 1;
batch.Analysis.done = 1;