WiscPlan_olderMV/photonDoseCalc/scripts_m/createFrames.m

 function createFrames()
 
%%%%%%%%%%%%%%%%%%   DLB created 5/21/07   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%   VERSION 2.3
%
%   Updated: 2/23/09
%
%   USEAGE:    >> createFrames *hit Enter* :p
%
%   DEPENDENCIES:
%       - you need a C:\Data folder (you should have this in Jeraj's grp
%       - need a data set WITH a .header file that was obtained using
%         Robert Pyzalski's adv2fl, adv2float, or Get_image program
%
%   WHAT IT DOES:
%   this function converts anything from pyzalski's script into amira format
%   and puts the .am files in their appropriate places.  
%   breaks up dynamic (4D) PET scans of any size and
%   correctly writes them as SUV or MBq/ml into Amira format regardless 
%   of: the number of frames, pixel size, FOV size, recon grid. Currently 
%   only C-11, F-18, Cu-61, and Cu-64 tracers have been put in.  It
%   shouldn't be too much trouble to add others if ever the need arises.
%
%   YES I'M AWARE THAT I DON'T APPLY THE 1/2 VOXEL SHIFT TO THE CT
%   Change amiraCTWriter if it bothers you.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%   CHANGES to createFrames:
%
%   VERSION 2.3
%   edit: removed the char(13) problem from certain headers that add extra 
%         carrage returns, Ngoneh spotted it
%       - I changed the syntax that searches through the header files
%   DLB - 2/23/09
%
%   VERSION 2.2
%   edit: Matt V pointed out MBq to mCi conversion still incorrect
%       - from *0.037 to /37. Finally correct
%       - FIXED 'static' and 'dynamic' string length bug that would ignore
%         any 'static' scan mode. Used 'else' to rename scan_mode for 'static'
%         cases. WILL NOT WORK with strcmp for future reference.
%   DLB - 1/6/09
%
%   VERSION 2.1
%   edit: Matt V noted that my MBq to mCi conversion was incorrect
%       - fixed both from *0.037 to /37  dumb mistake
%   DLB - 11/5/08
%
%   edit: Added stuff to the GUI that automatically updates
%       - mCi and uCi values for Matt V
%       - SUV factor for awesomeness
%   DLB - 10/24/08
%
%   edit: 
%       - Fixed flipz for all the PET's
%       - Added a mCi indicator to GUI 
%       - Changed injection time and scan start times
%   DLB - 10/23/08
%
%   VERSION 2.0
%   edit: After renaming this createStatic, I've switched back because I 
%   like createFrames better (as does everyone else). Now the program: 
%       - reads any size CT (converts them to shorts, thanks Keisha).
%       - has a nice SUV GUI with units and matching colours
%       - automatically flips the z dimension without asking
%       - added amiraCTWriter, amiraWriter, and checkHeader
%       - still need to write the WriteToHeader function!! lazy lazy
%   DLB - 10/17/08
%
%   VERSION 1.0
%   edit: Added the _SUV_fr and _MBq_fr to the file ID (fid).
%   DLB - 12/13/07
%
%   edit: Keisha pointed out the SUV calc was wrong along with a host of
%   other problems (radionuclide_name, logical check). I removed the ~
%   from logical and all seems to work fine.
%   DLB - 12/12/07
%
%   edit: now added error messages and changes in case the header file has 
%   insufficient information for the SUV calculation. cut out a bunch of
%   redundant code.
%   DLB - 11/28/07
%   
%   edit: now the ultimate... prompts you for MBq/ml or SUV values.
%   also prompts you for z-flipping.  correctly decay corrects residual 
%   to the initial syringe measurement, then corrects that value to the 
%   start of the scan.  all this is done by reading the header.  no
%   more createFrames('flip')!  won't work!
%   DLB - 11/27/07
%
%   edit: added varargin to handle flipdim(?,3).
%         usage: createFrames('flip')             - DLB 9/20/07
%                or createFrames  <enter> for regular mode
%
%         future will put in 'SUV' option as well
%
%   edit: added half a voxel length to amira images, b/c that's how amira
%   reads them in.  we've been doing it wrong all along!! - DLB 9/20/07
%
%   edit: Changed the XYZBox in writing to Amira such that
%   everything is centered relative to a 50 cm CT FOV.  ex. a 38 cm FOV is
%   centered so that it is in the center of the bounding box. - DLB 9/20/07
%         ____________        ____________
%        |      |     |      |   ______   |
%        |  30  |     |  to  |  |      |  |
%        |______|     |      |  |  30  |  |
%        |         50 |      |  |______|  | <-- 50 cm
%        |____________|      |____________|
%
%   edit: Super huge update.  Can now read multiple or single files of any 
%         size file input without running out of memory!!  256x256 for 33 
%         frames tested, works. This thing can handle it all now - DLB
%         9/(18-19)/07
%   edit: now can read 1 file at a time again isa() - DLB 9/18/07
%   edit: now reads multiple files at once - DLB 9/16/07
%   edit: reads 4 unit frames e.g. 1120 - DLB summer 07
%   edit: reads header info now - DLB 5/22/07
%
%       STOLE THE fprintp stuff from RTF's geom2am.m
%

warning off;
s = pwd;
cd C:\Data\

%% here I'm just going to flip everything by default, uncomment the dialog for else
% flip = questdlg('Flip the z dimension for everything you select?','Z-flip','Yes','No','Cancel');
flip = 'Yes';

% GUI for picking your .img files
[filename, pathname, filterindex] = uigetfile({'*.img';'*.*'},'File Selector','Multiselect','on');
if isequal(filename,0)
   disp('User selected Cancel')
   fclose all
   return
else
   if isa(filename,'cell')
       for k = 1:length(filename)
           disp(['User selected ', fullfile(pathname, filename{k})]) 
           leng = length(filename);
       end
   else
       disp(['User selected ', fullfile(pathname, filename)])
        leng = 1;
   end
end

for numFile = 1:leng
    header_filename = filename;    
    % open the .img file and associated .header file
    if isa(filename,'cell')
        header_fid = fopen([pathname strrep(header_filename{numFile},'.img','.header')],'r','ieee-be');
        fil = filename{numFile};
    else
        header_fid = fopen([pathname strrep(header_filename,'.img','.header')],'r','ieee-be');
        fil = filename;
    end
    header_num = fread(header_fid,inf);
    header = char(header_num(find(header_num~=13)))';
    
    % find dimensions of image
    modality = header(findstr(header,'modality = ')+11:findstr(header,'scan_mode = ')-2);
    XCount = str2num(header(findstr(header,'x_dim = ')+7:findstr(header,'y_dim')-2));
    YCount = str2num(header(findstr(header,'y_dim = ')+8:findstr(header,'z_dim')-2));
    ZCount = str2num(header(findstr(header,'z_dim = ')+8:findstr(header,'x_pixdim')-2));
    xpixdim = str2num(header(findstr(header,'x_pixdim = ')+11:findstr(header,'y_pixdim = ')-2));
    ypixdim = str2num(header(findstr(header,'y_pixdim = ')+11:findstr(header,'z_pixdim = ')-2));
    zpixdim = str2num(header(findstr(header,'z_pixdim = ')+11:findstr(header,'plane_thickness')-2));

    % I dont' know why I put this in.  CT doesn't write 'scan_mode =' maybe?
    if isempty(modality)
        modality = header(findstr(header,'modality = ')+11:findstr(header,'image1_datetime = ')-2);
    end
    
    switch modality 
        case 'CT'
            cd(pathname);
            cd('..');
            if exist('Formatted','dir') ~= 7 
                mkdir Formatted
            end 
            cd('Formatted');
            data = reshape(fread(fopen([pathname fil],'r','ieee-be'),inf,'float=>short'),XCount,YCount,ZCount);
            if strcmp(flip,'Yes')
                data = flipdim(data,3);
            end 
            amiraCTWriter(data,strrep(fil,'.img','.am'),xpixdim,ypixdim,zpixdim,XCount,YCount,ZCount,xpixdim*XCount,zpixdim*ZCount);
        case 'PET'   % this can only be a string of 2 characters for comparison to 'CT'
            voxel_value = questdlg(['Output voxel values for: ' fil],'Voxel Values','SUV','MBq/ml','Both','Cancel');
            scan_mode = header(findstr(header,'scan_mode = ')+12:findstr(header,'radionuclide_name = ')-2);
            % check to see if scan is dynamic or static
            if strcmp(scan_mode,'dynamic')
                frames = str2num(header(findstr(header,'number_of_frames = ')+18:findstr(header,'scan_datetime')-2));
                ZCount = ZCount/frames;  % should always be 35 b/c # of axial PET slices
            else
                scan_mode = 'static';
            end                       

            % you need to make sure voxel_value is only 3 elements long for
            % the OR if statements later on.  stupid need to find a more
            % elegent fix.
            switch length(voxel_value)
                case 4
                    voxel_value = 'Bot';
                case 6
                    voxel_value = 'MBq';
            end
      
            if ((strcmp(voxel_value,'SUV')) | (strcmp(voxel_value,'Bot')))
                if isempty(findstr(header,'patient_wt (kg)'))
                    patient_wt = 0;
                    tracer_activity = str2num(header(findstr(header,'tracer_activity = ')+17:findstr(header,'meas_datetime')-2));
                else
                    patient_wt = str2num(header(findstr(header,'patient_wt (kg) = ')+17:findstr(header,'meas_datetime')-2));
                    tracer_activity = str2num(header(findstr(header,'tracer_activity = ')+17:findstr(header,'patient_wt (kg) = ')-2));
                end
                meas_datetime = header(findstr(header,'meas_datetime')+27:findstr(header,'pre_inj_volume')-2);
                meas_datetime = meas_datetime(find((1-isspace(meas_datetime))));  % sparses the string (removes any spaces)
                scan_datetime = header(findstr(header,'scan_datetime = ')+27:findstr(header,'frame1_date')-2);
                scan_datetime = scan_datetime(find((1-isspace(scan_datetime))));  % sparses the string (removes any spaces)
                admin_datetime = header(findstr(header,'admin_datetime = ')+28:findstr(header,'post_inj_activity')-2);
                admin_datetime = admin_datetime(find((1-isspace(admin_datetime))));  % sparses the string (removes any spaces)
                post_inj_activity = str2num(header(findstr(header,'post_inj_activity = ')+20:findstr(header,'post_inj_datetime')-2));
                post_inj_datetime = header(findstr(header,'post_inj_datetime = ')+ 31:findstr(header,'decay_corr')-2);
                post_inj_datetime = post_inj_datetime(find((1-isspace(post_inj_datetime))));  % sparses the string (removes any spaces)
                radionuclide_name = header(findstr(header,'radionuclide_name = ')+20:findstr(header,'tracer_name')-2);
                radionuclide_name = radionuclide_name(find((1-isspace(radionuclide_name))));  % sparses the string (removes any spaces)
                
                if isempty(meas_datetime)
                    meas_datetime = '00:00:00';
                end
                if isempty(admin_datetime)
                    admin_datetime = '00:00:00';
                end
                if isempty(post_inj_datetime)
                    post_inj_datetime = '00:00:00';
                end
                
                [status,patient_wt, tracer_activity, meas_datetime, scan_datetime, admin_datetime, post_inj_activity, post_inj_datetime, radionuclide_name] = checkHeader(fil,patient_wt, tracer_activity, meas_datetime, scan_datetime, admin_datetime, post_inj_activity, post_inj_datetime, radionuclide_name);                
               
                % stop this program if the gui heard "cancel"
                if status == 'kill'
                    disp('Cancelled at header GUI');
                    return
                end
                       
                % finding the time difference between the measured activity
                % time and the residual measured time, in seconds
                delta_hr = (str2num([post_inj_datetime(1) post_inj_datetime(2)])-str2num([meas_datetime(1) meas_datetime(2)]))*3600;
                delta_min = (str2num([post_inj_datetime(4) post_inj_datetime(5)])-str2num([meas_datetime(4) meas_datetime(5)]))*60;
                delta_sec = (str2num([post_inj_datetime(7) post_inj_datetime(8)])-str2num([meas_datetime(7) meas_datetime(8)]));
                delta_time = delta_hr + delta_min + delta_sec;
                switch radionuclide_name
                    % all half life in sec
                    case '61Cu'
                        t_half = 3.333*3600;  
                    case '18F'
                        t_half = 6588;
                    case '64Cu'
                        t_half = 45720;
                    case '11C'
                        t_half = 20.334*60;
                end
     
                % correcting the measured syringe activity by subtracting
                % off the decay corrected residual activity
                true_inj_activity = tracer_activity - post_inj_activity*exp(delta_time*log(2)/t_half);
    
                % finding the time difference between the measured activity
                % time and the start of the scan
                scan_delta_hr = (str2num([scan_datetime(1) scan_datetime(2)])-str2num([meas_datetime(1) meas_datetime(2)]))*3600;
                scan_delta_min = (str2num([scan_datetime(4) scan_datetime(5)])-str2num([meas_datetime(4) meas_datetime(5)]))*60;
                scan_delta_sec = (str2num([scan_datetime(7) scan_datetime(8)])-str2num([meas_datetime(7) meas_datetime(8)]));
                scan_delta_time = scan_delta_hr + scan_delta_min + scan_delta_sec;
    
                % decay correcting the injected dose to the start of the scan
                true_inj_activity_at_scan_start = true_inj_activity*exp(-scan_delta_time*log(2)/t_half);

                %prepare to open and write the PET_SUV
                cd(pathname)
                cd('..')
                if exist('Processed','dir') ~= 7 
                    mkdir Processed
                end
                cd Processed
                
                
                switch scan_mode
                    case 'dynamic'
                        if exist('frames','dir') ~= 7 
                            mkdir frames;
                        end 
                        cd frames
                        file_id = fopen([pathname fil],'r','ieee-be');
                        for t = 1:frames
                            data = reshape(fread(file_id,XCount*YCount*ZCount,'float'),XCount,YCount,ZCount);
                            data = data./(true_inj_activity_at_scan_start/(patient_wt*1000));                
                            if strcmp(flip,'Yes')
                                data = flipdim(data,3);
                            end
                            amiraWriter(data,[strrep(fil,'.img','_SUV_fr') int2str(t) '.am'],xpixdim,ypixdim,zpixdim,XCount,YCount,ZCount,xpixdim*XCount,zpixdim*ZCount);
                        end
                    case 'static'
                        data = reshape(fread(fopen([pathname fil],'r','ieee-be'),inf,'float'),XCount,YCount,ZCount);
                        data = data./(true_inj_activity_at_scan_start/(patient_wt*1000));                
                        if strcmp(flip,'Yes')
                            data = flipdim(data,3);
                        end
                        amiraWriter(data,strrep(fil,'.img','_SUV.am'),xpixdim,ypixdim,zpixdim,XCount,YCount,ZCount,xpixdim*XCount,zpixdim*ZCount);
                end
                clear data;
            end

        if ((strcmp(voxel_value,'MBq')) | (strcmp(voxel_value,'Bot')))
                %prepare to open and write the PET_SUV
                cd(pathname)
                cd('..')
                if exist('Formatted','dir') ~= 7 
                    mkdir Formatted
                end 
                cd Formatted
                switch scan_mode
                    case 'dynamic'
                        fseek(header_fid,findstr(header,'number_of_frames')+18,'bof');
                        frames = str2num(char(fread(header_fid,findstr(header,'scan_datetime')-findstr(header,'number_of_frames')-20,'char')'));
                        if exist('frames','dir') ~= 7 
                            mkdir frames
                        end
                        cd frames
                        file_id = fopen([pathname fil],'r','ieee-be');
                        for t = 1:frames
                            data = reshape(fread(file_id,XCount*YCount*ZCount,'float'),XCount,YCount,ZCount);
                            if strcmp(flip,'Yes')
                                data = flipdim(data,3);
                            end
                            amiraWriter(data,[strrep(fil,'.img','_MBq_fr') int2str(t) '.am'],xpixdim,ypixdim,zpixdim,XCount,YCount,ZCount,xpixdim*XCount,zpixdim*ZCount);
                        end
                    case 'static'
                        data = reshape(fread(fopen([pathname fil],'r','ieee-be'),inf,'float'),XCount,YCount,ZCount);
                        if strcmp(flip,'Yes')
                            data = flipdim(data,3);
                        end
                        amiraWriter(data,strrep(fil,'.img','_MBq.am'),xpixdim,ypixdim,zpixdim,XCount,YCount,ZCount,xpixdim*XCount,zpixdim*ZCount);
                        clear data;
                end
        end
    end
end
fclose all;
cd(s);
 end 

%% BELOW ARE FUNCTIONS THAT THIS PROGRAM NEEDS TO EXECUTE %%
% 
% DO NOT MESS WITH THESE OR YOU WILL INCUR MY WRATH!!!
%
% amiraWriter
% amiraCTWriter
% checkHeader
%
%       Seriously, hands off!!!
%
%% amiraWriter
function amiraWriter(data,filename,dx,dy,dz,M,N,P,FOV,zFOV)
    fid = fopen([filename],'w');
    fprintf(fid,'# AmiraMesh 3D BINARY 2.0\n\n');
    fprintf(fid,['# CreationDate: ' datestr(now,'ddd mmm') datestr(now,' dd HH:MM:SS yyyy') '\n\n']);
    fprintf(fid,'define Lattice %g %g %g\n\n',M,N,P);
    fprintf(fid,'Parameters {\n');
    fprintf(fid,'    Content "%gx%gx%g %s, uniform coordinates",',M,N,P,'float');
    fprintf(fid,'    BoundingBox %g %g %g %g %g %g,\n',(50-FOV)/2+dx/2,50-(50-FOV)/2-dx/2,(50-FOV)/2+dy/2,50-(50-FOV)/2-dy/2,0,zFOV-dz);
    fprintf(fid,'    CoordType "uniform"\n');
    fprintf(fid,'}\n\n');
    fprintf(fid,'Lattice { %s Data } @1\n\n','float');
    fprintf(fid,'# Data section follows\n');
    fprintf(fid,'@1\n');
    fclose(fid);  % close the text part of the file
    fid = fopen([filename],'ab','ieee-be');
    fwrite(fid,data(:,:,:),'float');
    fclose(fid);
    disp(['Wrote to ' filename]);
end
 
%% amiraCTWriter
function amiraCTWriter(data,filename,dx,dy,dz,M,N,P,FOV,zFOV)
    fid = fopen([filename],'w');
    fprintf(fid,'# AmiraMesh 3D BINARY 2.0\n\n');
    fprintf(fid,['# CreationDate: ' datestr(now,'ddd mmm') datestr(now,' dd HH:MM:SS yyyy') '\n\n']);
    fprintf(fid,'define Lattice %g %g %g\n\n',M,N,P);
    fprintf(fid,'Parameters {\n');
    fprintf(fid,'    Content "%gx%gx%g %s, uniform coordinates",',M,N,P,'short');
    fprintf(fid,'    BoundingBox %g %g %g %g %g %g,\n',0,FOV-dx,0,FOV-dy,0,zFOV-dz);
    fprintf(fid,'    CoordType "uniform"\n');
    fprintf(fid,'}\n\n');
    fprintf(fid,'Lattice { %s Data } @1\n\n','short');
    fprintf(fid,'# Data section follows\n');
    fprintf(fid,'@1\n');
    fclose(fid);  % close the text part of the file
    fid = fopen([filename],'ab','ieee-be');
    fwrite(fid,data(:,:,:),'short');
    fclose(fid);
end

%% checkHeader
function [status,patient_wt, tracer_activity, meas_datetime, scan_datetime, injection_time, post_inj_activity, post_inj_datetime, radionuclide_name] = checkHeader(study_name,patient_wt,tracer_activity,meas_datetime,scan_datetime,injection_time,post_inj_activity,post_inj_datetime,radionuclide_name)
    global okay_val
    global cancel_val
    global writeit_val
    okay_val = 0;
    cancel_val = 0;
    writeit_val = 0;
    status = 1;  % this tells createStatic to stop trying to process data. status = 'kill'
    gui = figure('Position',[700,500,310,303]);
    patient_ID_txt = uicontrol('Style','text','String','Patient ID:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8 272 80 20]);
    patient_ID = uicontrol('Style','text','String',study_name,'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[92 272 180 20]);
    patient_wt_txt = uicontrol('Style','text','String','Patient Weight:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8 246 80 20]);
    patient_wt_units = uicontrol('Style','text','String','kgs','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 246 25 20]);    
    tracer_activity_txt = uicontrol('Style','text','String','Tracer Activity:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8 220 80 20]);

    % all the txt in the gui
    meas_datetime_units = uicontrol('Style','text','String','MBq @','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 220 35 20]);
    meas_datetime_mCi = uicontrol('Style','text','String','mCi','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 194 35 20]);
    scan_datetime_time = uicontrol('Style','text','String','hh:mm:ss','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[246 220 46 20]);    
    scan_datetime_txt = uicontrol('Style','text','String','Scan Start Time:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8 168 80 20]);
    scan_datetime_hh = uicontrol('Style','text','String','hh:mm:ss','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 168 46 20]);    
    injection_time_txt = uicontrol('Style','text','String','Injection Time:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8,142,80,20]);
    scan_datetime_txt2 = uicontrol('Style','text','String','hh:mm:ss','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 142 46 20]);    
    post_inj_activity_txt = uicontrol('Style','text','String','Post Inj Activity:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8 116 80 20]);
    post_inj_datetime_txt = uicontrol('Style','text','String','MBq @','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150,116,35,20]);
    post_inj_datetime_time = uicontrol('Style','text','String','hh:mm:ss','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[246 116 46 20]);        
    post_inj_datetime_uCi = uicontrol('Style','text','String','uCi','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 90 35 20]);
    radionuclide_name_txt = uicontrol('Style','text','String','Radionuclide:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8,64,80,20]);
    radionuclide_name_txt2 = uicontrol('Style','text','String','ex: 18F or 61Cu','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left','Position',[150 64 80 20]);
    SUV_factor_txt = uicontrol('Style','text','String','SUV Factor:','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right','Position',[8,38,80,20]);

    % all the editable fields
    patient_wt_var = uicontrol('Style','edit','String',patient_wt,'BackgroundColor','white','Position',[92 250 55 20]);
    tracer_activity_var = uicontrol('Style','edit','String',tracer_activity,'BackgroundColor','white','Position',[92 224 55 20]);
    tracer_activity_mCi = uicontrol('Style','text','String',num2str(tracer_activity/37),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','center','Position',[92 194 55 20]);
    meas_datetime_var = uicontrol('Style','edit','String',meas_datetime,'BackgroundColor','white','Position',[188 224 55 20]);
    scan_datetime_var = uicontrol('Style','edit','String',scan_datetime,'BackgroundColor','white','Position',[92 172 55 20]);
    injection_time_var = uicontrol('Style','edit','String',injection_time,'BackgroundColor','white','Position',[92 146 55 20]);
    post_inj_activity_var = uicontrol('Style','edit','String',post_inj_activity,'BackgroundColor','white','Position',[92 120 55 20]);
    post_inj_datetime_var = uicontrol('Style','edit','String',post_inj_datetime,'BackgroundColor','white','Position',[188 120 55 20]);
    post_inj_activity_uCi = uicontrol('Style','text','String',num2str(post_inj_activity/37*1000),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','center','Position',[92 90 55 20]);
    radionuclide_name_var = uicontrol('Style','edit','String',radionuclide_name,'BackgroundColor','white','Position',[92 68 55 20]);


    okay = uicontrol('Style','pushbutton','String','Okay','Position',[25,5,70,25],'Callback',@okay_Callback);
    cancel = uicontrol('Style','pushbutton','String','Cancel','Position',[105,5,70,25],'Callback',@cancel_Callback);
    writeit = uicontrol('Style','pushbutton','String','Write to header','Position',[185,5,100,25],'Callback',@writeit_Callback);
 
    wait_for_it = 0;
    while wait_for_it == 0
        pause(1);  % listen for a button push

        % listen for updates to Tracer Activity and update the mCi box
        tracer_activity = str2num(get(tracer_activity_var,'String'));
        tracer_activity_mCi = uicontrol('Style','text','String',num2str(tracer_activity/37),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','center','Position',[92 194 55 20]);
        post_inj_activity = str2num(get(post_inj_activity_var,'String'));
        post_inj_activity_uCi = uicontrol('Style','text','String',num2str(post_inj_activity/37*1000),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','center','Position',[92 90 55 20]);

%% this part calculates the SUV factor with the parameters shown
        tracer_activity = str2num(get(tracer_activity_var,'String'));
        post_inj_activity = str2num(get(post_inj_activity_var,'String'));
        radionuclide_name = get(radionuclide_name_var,'String');
        post_inj_datetime = get(post_inj_datetime_var,'String');
        meas_datetime = get(meas_datetime_var,'String');
        scan_datetime = get(scan_datetime_var,'String');
        patient_wt = str2num(get(patient_wt_var,'String'));
        % finding the time difference between the measured activity
        % time and the residual measured time, in seconds
        delta_hr = (str2num([post_inj_datetime(1) post_inj_datetime(2)])-str2num([meas_datetime(1) meas_datetime(2)]))*3600;
        delta_min = (str2num([post_inj_datetime(4) post_inj_datetime(5)])-str2num([meas_datetime(4) meas_datetime(5)]))*60;
        delta_sec = (str2num([post_inj_datetime(7) post_inj_datetime(8)])-str2num([meas_datetime(7) meas_datetime(8)]));
        delta_time = delta_hr + delta_min + delta_sec;
        switch radionuclide_name
            case '61Cu'
                t_half = 3.333*3600;  % half life in sec
            case '18F'
                t_half = 6588;
            case '64Cu'
                t_half = 45720;
            case '11C'
                t_half = 20.334*60;
        end
     
        % correcting the measured syringe activity by subtracting
        % off the decay corrected residual activity
        true_inj_activity = tracer_activity - post_inj_activity*exp(delta_time*log(2)/t_half);

        % finding the time difference between the measured activity
        % time and the start of the scan
        scan_delta_hr = (str2num([scan_datetime(1) scan_datetime(2)])-str2num([meas_datetime(1) meas_datetime(2)]))*3600;
        scan_delta_min = (str2num([scan_datetime(4) scan_datetime(5)])-str2num([meas_datetime(4) meas_datetime(5)]))*60;
        scan_delta_sec = (str2num([scan_datetime(7) scan_datetime(8)])-str2num([meas_datetime(7) meas_datetime(8)]));
        scan_delta_time = scan_delta_hr + scan_delta_min + scan_delta_sec;

        % decay correcting the injected dose to the start of the scan
        true_inj_activity_at_scan_start = true_inj_activity*exp(-scan_delta_time*log(2)/t_half);

        SUV_factor = 1/(true_inj_activity_at_scan_start/(patient_wt*1000));                
        SUV_factor_var = uicontrol('Style','text','String',SUV_factor,'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','center','Position',[92 38 55 20]);    

        % Listen for hit
        if okay_val == 1
            patient_wt = str2num(get(patient_wt_var,'String'));
            tracer_activity = str2num(get(tracer_activity_var,'String'));
            meas_datetime = get(meas_datetime_var,'String');
            scan_datetime = get(scan_datetime_var,'String');
            injection_time = get(injection_time_var,'String');
            post_inj_activity = str2num(get(post_inj_activity_var,'String'));
            post_inj_datetime = get(post_inj_datetime_var,'String');
            radionuclide_name = get(radionuclide_name_var,'String');
            wait_for_it = 1;
            close(gui);
        end
        if cancel_val == 1
            disp('Cancel was hit');
            close(gui);
            wait_for_it = 1;
            status = 'kill';
            return
        end
        if writeit_val == 1
            disp('Cancel was hit');
            close(gui);
            wait_for_it = 1;
            return
        end
    end 
end

function okay_Callback(source,eventdata)
    global okay_val
    global cancel_val
    global writeit_val
    okay_val = 1;
    cancel_val = 0;
    writeit_val = 0;
end
 
function cancel_Callback(source,eventdata)
    global okay_val
    global cancel_val
    global writeit_val
    okay_val = 0;
    cancel_val = 1;
    writeit_val = 0;
end

function writeit_Callback(source,eventdata)
    global okay_val
    global cancel_val
    global writeit_val
    okay_val = 0;
    cancel_val = 0;
    writeit_val = 0;
    disp('Write to header dun work yet!');
end