Hi Conn Users,

I have been wanting to batch the gui setup using conn_batch. I m using conn 13 with spm8 and both gui and batch run without any errors, however, the results dont match. The only two things i m changing from defaults in both gui and batch is the following: Changing units from percent signal change to 'raw' and  i am doing only roi-roi analysis. I am not sure why the final correlation matrices are different. I am looking within the first level folder. Please advise. 


 Following is my code:

%% CONN batch using CONN_13

clc
clear all
close all
[dirlist]=textread('/Volumes/analysis/CONN/CONN_auto/data/file_list.txt','%s');% text file that contains the path to each subject's folders
addpath(genpath('/scripts/matlab_shared_toolboxes/conn/')) % CONN_13
spm8
%% CONN setup
batch.filename='CONN_auto.mat';
batch.Setup.isnew=1;
batch.Setup.overwrite='Yes';
batch.Setup.acquisitiontype=1;
batch.Setup.voxelmask=1;
batch.Setup.voxelresolution=1;
batch.Setup.nsubjects=9;
batch.Setup.RT=2;
batch.Setup.analyses=[1]; %Only ROI-to-ROI pipelines (changed from the default)
batch.Setup.analysisunits=2; % raw unit (changed from default: percent signal change)
batch.Setup.voxelresolution=1;
batch.Setup.roiextract=2;
batch.Setup.overwrite='Yes';
for isub=1:length(dirlist) %9
rootdir=dirlist{isub};
batch.Setup.functionals{isub}{1}= spm_select('ExtFPList',fullfile(rootdir,'Resting'),'^rest_dn_w.*s\.nii$',1:216);
batch.Setup.structurals{isub}=spm_select('ExtFPList',fullfile(rootdir,'anat'),'^wFSP.*R\.nii$');
batch.Setup.covariates.files{1}{isub}{1}=spm_select('FPList',fullfile(rootdir,'Resting'),'^art_regression_outliers_and_movement.*\.mat$');
batch.Setup.covariates.names={'motionart'};
batch.Setup.conditions.names={'rest'};
batch.Setup.conditions.onsets{1}{isub}{1}=0; batch.Setup.conditions.durations{1}{isub}{1}=inf; % rest condition (all sessions)
end
batch.Setup.done=1;
%% CONN preprocessing (all defaults)
batch.Preprocessing.filter=[0.0080, 0.0900];
batch.Preprocessing.detrending=1;
batch.Preprocessing.despiking=1;
batch.Preprocessing.overwrite='Yes';
batch.Preprocessing.done=1;
%% CONN Analysis (all defaults)
batch.Analysis.done=1;
batch.Analysis.overwrite='Yes';
%% Run the batch
conn_batch(batch)