Initial commit.

Copies 0 ms spin lock time files to new directory.

Author: mggardne

T1rho_slt0.m

@@ -0,0 +1,111 @@
+%#######################################################################
+%
+%                  * 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