OPTIMA_repair_BIDS_1_0_2_dwi3.m

 function BIDS = OPTIMA_repair_BIDS_1_0_2_dwi3(input_dir)
% 
% Repair dwi3 (pepolar)
% here, manual stopping of acquisition leaves dicom slices of an incomplete
% last volume. These interfer with dcm2niix and therefore need to be
% deleted
%
% Required fields of repair_BIDS_1_0_2_dwi2:
%
% input_dir  -  location of the GE data, use absolute path
%
%               data must have passed consistency checks using
%               consistency.m in MICHA_TEST/FA_consistency
%               the script is expecting a file named
%               "biomax_out_*_VERIFIED*.txt" or
%               "biomax_out_*_MODIFIED*.txt" 
%               to be present in the subjects main directory
% 
% directories must be known:
% addpath '/run/media/spectro/DATAPART1/OPTIMA/autoscripts_BIDS'
%
% function call, e.g.: OPTIMA_repair_BIDS_1_0_2_dwi3('/run/media/spectro/DATAPART1/OPTIMA/Garching2/PTP0070_T7')
%
% structure BIDS
% input.dir     - directory with verified data
%           e.g. BIDS.input.dir = '/run/media/spectro/DATAPART1/OPTIMA/Garching2/PTP0070_T7'
% input.biomax  - biomax_out filename
%
% file history:
% created M. Czisch 29.5.2020
% to repair BecomeVersion 1.0.2
% adapted for OPTIMA 13.11.2020
% vers 3: includes cases without SIT; 16.11.2020

fprintf('\nRepair BIDS \n');

clear BIDS
BIDS.input.dir = input_dir;
BIDS.output.dir = '';
BIDS.autoscripts.dir = '/run/media/spectro/DATAPART1/OPTIMA/autoscripts_BIDS';

% have the data being for consistency checked already?
% does biomax_out exist?

BIDS = OPTIMA_check_BIOMAX(BIDS);


% check and prepare temporary BIDS directory structure

pathInfo = what(BIDS.input.dir);
current_dir = pathInfo.path;
tmp_str = strsplit(current_dir,'/');
BIDS.output.dir = [current_dir,'/',tmp_str{end},'_BIDS'];

if ~exist(BIDS.output.dir)
    mkdir(BIDS.output.dir);
    mkdir([BIDS.output.dir,'/dwi']);
end

% load and format biomax_out info

biomax = load(BIDS.input.biomax);

if size(biomax,1) == 8 % version without SIT
    biomax_table = array2table(biomax,...
        'VariableNames',{'Ser','Log','EDF','PPG'},...
        'RowNames',{'Loc';'T1w';'Cal';'rest1';...
        'EPI1';'FLAIR';...
        'DTI';'Pepolar'});
elseif size(biomax,1) == 9 % newer version including SIT
    biomax_table = array2table(biomax,...
        'VariableNames',{'Ser','Log','EDF','PPG'},...
        'RowNames',{'Loc';'T1w';'Cal';'rest1';...
        'EPI1';'FLAIR';'SIT1';...
        'DTI';'Pepolar'});
else
    fprintf('\nwrong biomax size\n');
end

            
% read content of GE EXAM and SERIES files

BIDS = OPTIMA_read_GE_BIDS_4(BIDS);


% do repair

cd(input_dir);
OPTIMA_repair_convert_GE_dwi2_to_BIDS(BIDS, biomax_table);


fprintf('\n\ndone repair of %s\n', BIDS.input.data_dir(1).PatientID{3});

clear all