bsc_GenROIfromPairStringList_BL.m

function bsc_GenROIfromPairStringList_BL()
% bsc_genNiftiROIfromStringList(feORwbfg,atlas,ROIstring, smoothKernel)
%
% Given a string list of rois (in the specified format) loops over
% the list and generates nifti ROI files for each 
%
%  INPUTS:
%  -feORwbfg: either a string or an object, to either a wbFG or an FE
%  structure
%
%  -atlas: path to an atlas or an atlas.
%
%  -ROIstring:  a string list of atlas based roi specifications from the
%  atlas that you would like merged into a single ROI.  eg: '2 56 30 54; 34
%  654 \n 25 45 56; 23 \n 456 34; 35 75'.  Must correspond to the values in
%  the atlas nifti itself.
%
%  OUTPUTS: 
% -classification: 
%  The strucure has a field "names" with (N) names of the tracts classified
%  while the field "indexes" has a j long vector (where  j = the nubmer of
%  streamlines in wbFG (i.e. length(wbFG.fibers)).  This j long vector has
%  a 0 for to indicate a streamline has gone unclassified, or a number 1:N
%  indicatate that the streamline has been classified as a member of tract
%  (N).
%
%  NOTE:  Makes a call to mri_convert, so requires that FreeSurfer be
%  installed and set up properly.
%
%  (C) Daniel Bullock 2018 Bloomington, Indiana
%% Begin code

 if ~isdeployed
     disp('adding paths');
     addpath(genpath('/N/soft/rhel7/spm/8')) %spm needs to be loaded before vistasoft as vistasoft provides anmean that works
     addpath(genpath('/N/u/brlife/git/jsonlab'))
     addpath(genpath('/N/u/brlife/git/vistasoft'))
     addpath(genpath('/N/u/brlife/git/wma_tools'))
 end

%config = loadjson('/N/dc2/projects/lifebid/HCP/Dan/GitStoreDir/ROIs2ROIsSegment/config.json');
config = loadjson('config.json')

ROIstring=config.roiPairs;
smoothKernel=config.smoothKernel;

if isfield(config,'atlas')
       atlas=config.atlas
end

if isfield(config,'ROI')
      ROIdir=config.ROI
end

%% gen ROI
fprintf('Generating ROIs for the following indicies: \n %s',ROIstring);
%just in case
ROIstring=strrep(ROIstring,'\n',newline);
ROIstring=strrep(ROIstring,';',newline);
stringCells = splitlines(ROIstring);
mkdir('roi/')

for iROIs=1:length(stringCells)
    ROInums=str2num(stringCells{iROIs});
    %% run the merge roi function
    if ~notDefined('atlas')
        mergedROI =bsc_roiFromAtlasNums(atlas,ROInums, smoothKernel);
               currROIName=fullfile(pwd,strcat('/roi/ROI',num2str(iROIs),'.nii.gz'));
        [~, ~]=dtiRoiNiftiFromMat (mergedROI,atlas,currROIName,1);
    elseif ~notDefined('ROIdir')
        for iROInums=1:length(ROInums)
            niiPaths{iROInums}=strcat(ROIdir,'ROI',num2str(ROInums(iROInums)),'.nii.gz');
        end
        if length(ROInums)>1
            
            mergedROI = niftiMerge(niiPaths, strcat('rois/ROI',strrep(num2str(ROInums),'  ','_'),'.nii.gz'));
        end
        currROIName=fullfile(pwd,strcat('/roi/ROI',num2str(iROIs),'.nii.gz'));
        fprintf('\n saving %s',currROIName)
        niftiWrite(mergedROI,currROIName)
    end
end
end