As part of a previous non-connectivity project I have used SPM12
and ART to process my functional data. Creation of first-level SPMs
included adding the ART-estimated motion and outlier regressors to
the design matrix (as well as condition onsets etc.). I have
applied there the high pass filter (128 seconds) and I have
included the HRF function. Finally, I have also estimated these
SPMs.
Now, in a new connectivity project we are using the same data
and looking at ROI 1) timeseries and 2) connectivity with the conn
toolbox. My question is - do I need to define new SPMs without the
ART regressors, high pass filter and HRF function or is my
exisiting code fine? My goal is to avoid doing the same processing
steps twice. Please note that I am looking at both the timeseries
and connectivity.
for s = 1
clc
disp(s)
cd(subcode(s,:))
% Point to the data
location
batch.filename=fullfile(pwd,'conn_Run1.mat');
STRUCTURAL_FILE = cellstr([root, filesep,
subcode(s,:), filesep,'T1/T1.nii']);
batch.Setup.structurals=STRUCTURAL_FILE;
SPM_FILE=
cellstr([root, filesep, subcode(s,:), filesep, 'results/SPM.mat']);
batch.Setup.spmfiles=SPM_FILE;
batch.Setup.nsubjects=1;
batch.Setup.RT=2.5;
% Add own ROIs
batch.Setup.rois.files{1} = [root,"/Schaefer2018_300Parcels_17Networks_order_FSLMNI152_2mm.nii"];
batch.Setup.rois.files{2} = [root, "AAL3.nii"];
batch.Setup.rois.multiplelabels=1;
batch.Setup.rois.add=1;
batch.Setup.isnew=1;
batch.Setup.done=1;
conn_batch(batch);
clear
batch
%
Denoising
batch.Denoising.filter=[0.009,
0.08];
batch.Denoising.done = 1;
conn_batch(batch);
clear
batch
%
ROI-to-ROI connectivity
batch.Analysis.name = 'RRC'; % name of the
analysis
batch.Analysis.analysis_number=1; % Sequential number identifying each set
of independent first-level analyses
batch.Analysis.measure=1; % connectivity measure used {1 =
'correlation (bivariate)', 2 = 'correlation (semipartial)', 3 =
'regression (bivariate)', 4 = 'regression
(multivariate)';
batch.Analysis.weight=2; % within-condition weight used {1 =
'none', 2 = 'hrf', 3 = 'hanning';
batch.Analysis.sources={'Schaefer2018_300Parcels_17Networks_order_FSLMNI152_2mm',
'AAL3'}; % (if empty then uses all ROIs contained
in spm12/toolboxes/conn/rois)
batch.Analysis.done=1;
conn_batch(batch);
cd(root)
clear
batch
end
