From c567e5af496857d5f8e5e0bd56b52b9b25faa6a8 Mon Sep 17 00:00:00 2001
From: Hiromasa Takemura <takemura@dhcp-177-235.nict.go.jp>
Date: Wed, 26 Aug 2020 15:09:51 +0900
Subject: [PATCH] Add functions enabling .tck export compatible with MRTrix3
 MRView

---
 fileFilters/mrtrix/dtiExportFibersMrtrix3.m | 92 +++++++++++++++++++++
 mrDiffusion/fiber/fg/fgWrite.m              |  5 +-
 2 files changed, 96 insertions(+), 1 deletion(-)
 create mode 100755 fileFilters/mrtrix/dtiExportFibersMrtrix3.m
 mode change 100644 => 100755 mrDiffusion/fiber/fg/fgWrite.m

diff --git a/fileFilters/mrtrix/dtiExportFibersMrtrix3.m b/fileFilters/mrtrix/dtiExportFibersMrtrix3.m
new file mode 100755
index 00000000..ff137b24
--- /dev/null
+++ b/fileFilters/mrtrix/dtiExportFibersMrtrix3.m
@@ -0,0 +1,92 @@
+function tck = dtiExportFibersMrtrix3(fg, tck_filename)
+%
+%   tck = dtiExportFibersMrtrix3(fg, tck_filename) 
+%
+%   Saves a FG structure to disk in MRTRIX format (.tck)
+%
+% INPUTS:
+%     fg -           vistasoft fiber group structure
+%     tck_filename - file path to output .ick
+% 
+% OUTPUT:
+%     tck - reconstructed TCK file structure. 
+%
+%   Based on MATLAB functions distributed with mrtrix 0.3
+%
+% This function is a modification of dtiExportFibersMrtrix.m, by incorportating header information of MRTrix 3 .tck format ("mrtrix tracks"). 
+%
+% Written by Hiromasa Takemura, CiNet BIT 2020 August 
+% 
+
+% initialize output
+tck = dtiGetFgParams(fg);
+
+% transpose the streamline order
+tck.data = fg.fibers';
+
+for ii = 1:length(tck.data)
+    % transpose the node order
+    tck.data{ii} = tck.data{ii}';
+
+end
+clear ii
+
+% save the file w/ mrtrix fxn
+write_mrtrix_fibers(tck, tck_filename);
+
+return
+end
+
+%%%%%%%%%%%%%%%%%%%%%%
+% AUXILIARY FUNCTION %
+%%%%%%%%%%%%%%%%%%%%%%
+function write_mrtrix_fibers (fibers, filename)
+%
+% function: write_mrtrix_fibers (fibers, filename)
+%
+% writes the track data stored as a cell array in the 'data' field of the
+% fibers variable to the MRtrix format track file 'filename'. All other fields
+% of the fibers variable will be written as text entries in the header, and are
+% expected to supplied as character arrays.
+%
+% 
+% This function was originally distributed with mrtrix 0.2/0.3
+
+if ~isfield (fibers, 'data')
+  disp ('ERROR: input fibers variable does not contain required ''data'' field');
+  return;
+end
+
+if ~iscell (fibers.data)
+  disp ('ERROR: input fibers.data variable should be a cell array');
+  return;
+end
+
+f = fopen (filename, 'w', 'ieee-le');
+if (f < 1) 
+  disp (['error opening ' filename ]);
+  return;
+end
+
+fprintf (f, 'mrtrix tracks\ndatatype: Float32LE\ncount: %d\n', prod(size(fibers.data)));
+names = fieldnames(fibers);
+for i=1:size(names)
+  if strcmpi (names{i}, 'data'), continue; end
+  if strcmpi (names{i}, 'count'), continue; end
+  if strcmpi (names{i}, 'datatype'), continue; end
+  fprintf (f, '%s: %s\n', names{i}, getfield(fibers, names{i}));
+end
+fprintf (f, '%s: %s\n', 'timestamp: ', num2str(now)); % This allows visualizing the streamlines in mrview
+data_offset = ftell (f) + 20;
+fprintf (f, 'file: . %d\nEND\n', data_offset);
+
+fwrite (f, zeros(data_offset-ftell(f),1), 'uint8');
+for i = 1:prod(size(fibers.data))
+  fwrite (f, fibers.data{i}', 'float32');
+  fwrite (f, [ nan nan nan ], 'float32');
+end
+
+fwrite (f, [ inf inf inf ], 'float32');
+fclose (f);
+
+end
\ No newline at end of file
diff --git a/mrDiffusion/fiber/fg/fgWrite.m b/mrDiffusion/fiber/fg/fgWrite.m
old mode 100644
new mode 100755
index cb459c85..8bad1dc4
--- a/mrDiffusion/fiber/fg/fgWrite.m
+++ b/mrDiffusion/fiber/fg/fgWrite.m
@@ -13,7 +13,8 @@ function fgWrite(fg,name,type)
 %             'pdb'    - quench file format [DEFAULT]
 %             'quench' - same as 'pdb'                      
 %             'mat'    - matlab file format
-%             'tck'    - MRTRIX file format (also 'mrtrix'/'.tck')
+%             'tck'    - MRTRIX3 file format (also 'mrtrix'/'.tck')
+%	      'tck2'   - MRTRIX version 0.2 file format
 %
 %          * If "name" ends in either .pdb or .mat the correct file type
 %            will be used.
@@ -69,6 +70,8 @@ function fgWrite(fg,name,type)
     case 'mat'
         dtiWriteFiberGroup(fg, name);
     case {'tck', 'mrtrix', '.tck'}
+        dtiExportFibersMrtrix3(fg, name);
+    case {'tck2'}
         dtiExportFibersMrtrix(fg, name);
 end