T1rho_slt0.m

%#######################################################################
%
%                  * T1rho Spin Lock Time 0 Program *
%
%          M-File which reads a dicom_lst MAT file and copies the zero
%     ms spin lock time files from the T1rho series to separate
%     directories.  The new directory(ies) is(are) DICOM_*, where *
%     is(are) the series number(s).  Also, creates a command/shell file
%     with the commands to copy the files.
%
%     NOTES:  1.  MAT file dicom_lst.MAT must be in the current working
%             directory.  See dicom_lst.m.
%
%             2.  Assumes the DICOM subdirectory is in the current
%             working directory.
%
%             3.  Assumes there are more than 10 and less than 100 MRI
%             slices through the knee.
%
%             4.  The shell files must be made executable (chmod +x)
%             and run from a terminal window (unix console).  The
%             command/batch file must be run with the run command or
%             in a command/DOS window.
%
%     15-Sep-2020 * Mack Gardner-Morse
%

%#######################################################################
%
% Load File Names and Other Variables
%
load dicom_lst afiles id im_type nimages ptxt sn splcktc;
%
fnams = afiles(id);     % Valid file names
%
% Find T1rho Series
%
idt1r = contains(ptxt,'3DMAPPS');
%
im_typ = im_type(id);   % Valid image types
%
id2 = ~contains(im_typ,'T1rho');
idt1r = idt1r&id2;
%
nt1r = sum(idt1r);
idt1r = find(idt1r);
%
nimags = nimages(id);   % Valid number of images for series
%
if ispc
  cmd0 = 'copy ';
  fext = '.bat';
  hdr = 'REM ';
  cm = 'REM';
else
  cmd0 = 'cp ';
  fext = '.sh';
  hdr = '#!/bin/sh';
  cm = '#'
end
%
for k = 1:nt1r
%
% Generate Operating System Commands
%
   id0 = idt1r(k);      % Series index
%
   slt = eval([ '[' splcktc{id0} ']' ]);    % Get spin lock times
   nslt = size(slt,2);  % Number of spin lock times
%   
   fnams0 = char(fnams{id0}(1:nslt:nimags(id0)));     % Files w/ 0 ms spin lock times
   nf = size(fnams0,1); % Number of files
%
   fn = int2str((1:nf)');              % File numbers
   fn = char(strrep(cellstr(fn),' ','0'));  % Replace space with zero
%
   sn_str = int2str(sn(id0));          % Series number as a string
   ddir = repmat([' DICOM_' sn_str '\IM_00'],nf,1);   % New directory
%
   cmds = [repmat(cmd0,nf,1) fnams0 ddir fn];    % DOS/shell commands
%
% Open Command/Shell File and Write Header Comments
%
   fid = fopen(['dicom_' sn_str fext],'wt');
   fprintf(fid,'%s\n',hdr);
   if ~ispc
     fprintf(fid,'%s\n',cm);
   end
   fprintf(fid,'%s\n',[cm ' Command/shell file for Series ' sn_str]);
   fprintf(fid,'%s\n',[cm ' Auto-generated by T1rho_slt0.m']);
   fprintf(fid,'%s\n',[cm ' ' date]);
   if ispc
     fprintf(fid,'%s',[cm ' ']);
   else
     fprintf(fid,'%s',cm);
   end
%
% Make Directory
%
   mddir = ['mkdir DICOM_' sn_str];
   eval(['!' mddir]);
   fprintf(fid,'\n%s',mddir);
%
% Execute and Write Commands
%
   for l = 1:nf
      eval(['!' cmds(l,:)]);
      fprintf(fid,'\n%s',cmds(l,:));
   end
%
end