Hi CONN expert(s),

I'm trying to use the standalone version of CONN, but couldn't figure out how to proceed. Not sure how to best filter this help forum for specific thread(s) on this topic, so decided to start one and any reference to past relevant posts is welcomed to avoid redundant info.

Specifically, I'm trying to use the standalone version to achieve something similar to that of conn_batch, because I'm using it for my current workaround with the matlab license. Would this be achievable?

Btw, I'm using conn_batch as follows for single subjects:
```
function conn_single(sub,scanner)
cwd=pwd;
FUNCTIONAL_FILE=cellstr(conn_dir([sub,'/EPI*.nii']));
STRUCTURAL_FILE=cellstr(conn_dir([sub,'/*-n4.nii']));
TR=3;

clear batch;
batch.filename=fullfile(cwd,['conn_',scanner,'_',sub,'.mat']); % New conn_*.mat experiment name
%% SETUP & PREPROCESSING step (using default values for most parameters, see help conn_batch to define non-default values)
% CONN Setup.preprocessing
batch.Setup.isnew=1;
batch.Setup.nsubjects=1;
batch.Setup.nsessions=1;
batch.Setup.RT=TR; % TR (seconds)
batch.Setup.functionals=repmat({{}},[1,1]); % Point to functional volumes
batch.Setup.functionals{1}{1}{1}=FUNCTIONAL_FILE{1};
batch.Setup.structurals=STRUCTURAL_FILE; % Point to anatomical volumes
batch.Setup.conditions.names={'rest'};
batch.Setup.preprocessing.steps={'functional_label_as_original',...
'functional_slicetime','functional_realign&unwarp','functional_center',...
'functional_art','structural_center','functional_segment&normalize_indirect',...
'functional_label_as_mnispace','functional_smooth','functional_label_as_smoothed'};
batch.Setup.preprocessing.sliceorder='interleaved (bottom-up)';
batch.Setup.preprocessing.art_thresholds=[3 .9];
batch.Setup.preprocessing.voxelsize_anat=1;
batch.Setup.preprocessing.fwhm=5;
batch.Setup.done=1;
batch.Setup.overwrite=1;

%% DENOISING step
% CONN Denoising
batch.Denoising.filter=[0.008, 0.09]; % frequency filter (band-pass, in Hz)
batch.Denoising.done=1;
batch.Denoising.overwrite=1;

%% FIRST-LEVEL ANALYSIS step
% CONN Analysis
batch.Analysis.done=1;
batch.Analysis.overwrite=1;
batch.vvAnalysis.done=1;
batch.vvAnalysis.overwrite=1;
batch.dynAnalysis.done=1;
batch.dynAnalysis.overwrite=1;
%% QA step
% CONN QA plots
batch.QA.plots={'QA_DENOISE histogram','QA_DENOISE timeseries',...
'QA_NORM functional','QA_NORM structural','QA_REG functional','QA_REG structural'};
batch.QA.foldername=[sub,'/results/qa'];
%% main
conn_batch(batch);
```
Separately from the standalone question above, I'm also interested in obtaining the functional connectivity 'bell' curve that shows before/after denoising effects in QA plots (attached) but not sure how it would be named, as for batch.QA.plots above.

Any insight would be greatly appreciated.

Shengwei