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ICA_template_pipeline.m
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ICA_template_pipeline.m
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function ICA_template_pipeline(maindir, fslpath, afnipath, antspath, fmriprepdir, firstlevdir, templatepath, comp_sel_thresholds, numcomps, comp_val_thresholds, activ_val_thresholds, taskname, icasmoothkernel, meanshiftclusterpath)
if(nargin==0)
maindir = '/home/mkrishnamu/Downloads/ICAmotor-main/';
spmpath = '/nas/data/app/spm12/';
fslpath = '/usr/local/software/FSL-6.0.3/fsl';
afnipath= '/usr/local/software/afni-2021_01';
antspath = '/hct/fmriprep/install/bin/antsApplyTransforms';
icasmoothkernel = 2.49; %Smoothing kernel to smooth fmriprep preprocessed rs-fMRI data in fsl
fmriprepdir='Data/'; %directory with fMRIprep outputs
comp_sel_thresholds = [1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6]; %list of thresholds used to select components that comprise the final map
numcomps = {'auto', '20', '30', '40', '50', '60'}; %list of Total Number of Components used to select components that comprise the final map
templatepath = 'Templates/HMAT_pre_post_central.nii';
templateMNIspace = 'MNI152NLin6Asym';
firstlevdir = 'FirstLevel/';
comp_val_thresholds = [1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6];%List of ICA map thresholds used to compare to task activation
activ_val_thresholds = [ 0.05 0.01 0.005 0.001];%List of task activation p value thresholds (assuming task activation is a t map)
taskname = 'motor';
meanshiftclusterfolderpath = '/hct/fmriprep/ICA/';
end
cd(maindir);
addpath(spmpath);
addpath(meanshiftclusterfolderpath);
wIMM_component_generation(fslpath, fmriprepdir, numcomps, icasmoothkernel);
wIMM_creation(antspath, afnipath, fmriprepdir, templatepath, comp_sel_thresholds, numcomps, templateMNIspace);
wIMM_task_validation(fmriprepdir, comp_val_thresholds, activ_val_thresholds, taskname, firstlevdir, afnipath);
end