internal_TL_analysis.m

function [obj] = internal_TL_analysis(...
        BOLD_fMRI_unsmoothed_data, ...
        BOLD_fMRI_Smoothed_data, ...
        runMotionParameters, ...
        FreeSurfer_segmentation_Atlas_path, ...
        FreeSurfer_Thalamic_Segmentation, ...
        participant_TL_task_log_path, ...
        subjectID, ...
        TR, ...
        left_AC_search_region_mask, ...
        right_AC_search_region_mask, ...
        left_VC_search_region_mask, ...
        right_VC_search_region_mask, ...
        intermediatesOutputDirectory, ...
        fROIoutputDirectory ...
        )

    if (~exist(intermediatesOutputDirectory,'dir'))
        mkdir(intermediatesOutputDirectory);
    end
    if (~exist(fROIoutputDirectory,'dir'))
        mkdir(fROIoutputDirectory);
    end

    obj.spmuse.TR = TR;
    obj.home = intermediatesOutputDirectory;
    obj.par.par.name = subjectID;
    obj.par.par.home = intermediatesOutputDirectory;
    obj.td.logs.source = participant_TL_task_log_path;

    obj.tMNI_run = BOLD_fMRI_unsmoothed_data;
    obj.stMNI_run = BOLD_fMRI_Smoothed_data;
    obj.MPfile_name_run = runMotionParameters;

    [Y_grayMatter_mask,V_grayMatter_mask, ...
        Y_whiteMatter_mask,Y_CSF_mask, ...
        grayMatterMask_eroded,whiteMatterMask_eroded,csfMask_eroded] = ...
        TLmakeMasks(FreeSurfer_segmentation_Atlas_path);

    % run all the main 6 functions of the pipeline.
    obj = TLreadLogs(obj , participant_TL_task_log_path);

    obj = TLprep1l(obj,Y_grayMatter_mask,V_grayMatter_mask);

    obj = TLrun1l(obj);

    obj = TLmakeSearchSpace(obj,FreeSurfer_Thalamic_Segmentation,FreeSurfer_segmentation_Atlas_path);

    obj = TLgetROIs(obj, ...
        left_AC_search_region_mask,right_AC_search_region_mask, ...
        left_VC_search_region_mask,right_VC_search_region_mask, ...
        Y_grayMatter_mask,Y_whiteMatter_mask,Y_CSF_mask,...
        grayMatterMask_eroded,whiteMatterMask_eroded,csfMask_eroded, ...
        intermediatesOutputDirectory, ...
        fROIoutputDirectory);

end