Merge pull request #2273 from MRtrix3/fixelconnectivity

fixelconnectivity: Enhancements
MRtrix3 · Jul 19, 2023 · 86eb1ea · 86eb1ea
2 parents 5a3a8bf + cdc1c3b
commit 86eb1ea
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Showing 10 changed files with 371 additions and 158 deletions.
diff --git a/cmd/fixelconnectivity.cpp b/cmd/fixelconnectivity.cpp
@@ -18,10 +18,12 @@
 #include "command.h"
 #include "fixel/fixel.h"
 #include "fixel/helpers.h"
-#include "fixel/index_remapper.h"
+
+#include "dwi/tractography/weights.h"
 #include "fixel/matrix.h"
 
 
+
 #define DEFAULT_ANGLE_THRESHOLD 45.0
 #define DEFAULT_CONNECTIVITY_THRESHOLD 0.01
 
@@ -60,7 +62,17 @@ void usage ()
     + Argument ("value").type_float (0.0, 90.0)
 
   + Option ("mask", "provide a fixel data file containing a mask of those fixels to be computed; fixels outside the mask will be empty in the output matrix")
-    + Argument ("file").type_image_in();
+    + Argument ("file").type_image_in()
+
+  + DWI::Tractography::TrackWeightsInOption
+
+  + OptionGroup ("Options for additional outputs to be generated")
+
+  + Option ("count", "export a fixel data file encoding the number of connections for each fixel")
+    + Argument ("path").type_image_out()
+
+  + Option ("extent", "export a fixel data file encoding the extent of connectivity (sum of weights) for each fixel")
+    + Argument ("path").type_image_out();
 
 }
 
@@ -69,6 +81,20 @@ using value_type = float;
 using Fixel::index_type;
 
 
+
+template <class WriterType>
+void set_optional_outputs (WriterType& writer)
+{
+  auto opt = get_options ("count");
+  if (opt.size())
+    writer.set_count_path (opt[0][0]);
+  opt = get_options ("extent");
+  if (opt.size())
+    writer.set_extent_path (opt[0][0]);
+}
+
+
+
 void run()
 {
   const value_type connectivity_threshold = get_option_value ("connectivity", value_type(DEFAULT_CONNECTIVITY_THRESHOLD));
@@ -96,14 +122,29 @@ void run()
       fixel_mask.value() = true;
   }
 
-  auto connectivity_matrix = Fixel::Matrix::generate (argument[1],
-                                                      index_image,
-                                                      fixel_mask,
-                                                      angular_threshold);
+  if (get_options ("tck_weights_in").size()) {
+
+    auto connectivity_matrix = Fixel::Matrix::generate_weighted (argument[1],
+                                                                index_image,
+                                                                fixel_mask,
+                                                                angular_threshold);
 
-  Fixel::Matrix::normalise_and_write (connectivity_matrix,
-                                      connectivity_threshold,
-                                      argument[2]);
+    Fixel::Matrix::Writer<Fixel::Matrix::InitMatrixWeighted> writer (connectivity_matrix, connectivity_threshold);
+    set_optional_outputs (writer);
+    writer.save (argument[2]);
+
+  } else {
+
+    auto connectivity_matrix = Fixel::Matrix::generate_unweighted (argument[1],
+                                                                  index_image,
+                                                                  fixel_mask,
+                                                                  angular_threshold);
+
+    Fixel::Matrix::Writer<Fixel::Matrix::InitMatrixUnweighted> writer (connectivity_matrix, connectivity_threshold);
+    set_optional_outputs (writer);
+    writer.save (argument[2]);
+
+  }
 
 }
 
diff --git a/core/app.h b/core/app.h
@@ -171,7 +171,7 @@ namespace MR
         if (check_overwrite_files_func)
           check_overwrite_files_func (name);
         else
-          throw Exception ("output file \"" + name + "\" already exists (use -force option to force overwrite)");
+          throw Exception ("output path \"" + name + "\" already exists (use -force option to force overwrite)");
       }
     }
 

diff --git a/core/fixel/helpers.h b/core/fixel/helpers.h
@@ -29,7 +29,7 @@
 namespace MR
 {
   class InvalidFixelDirectoryException : public Exception
-  { 
+  {
     public:
       InvalidFixelDirectoryException (const std::string& msg) : Exception(msg) {}
       InvalidFixelDirectoryException (const Exception& previous_exception, const std::string& msg)
@@ -306,6 +306,7 @@ namespace MR
       header.size(0) = nfixels;
       header.size(1) = 1;
       header.size(2) = 1;
+      header.spacing(0) = header.spacing(1) = header.spacing(2) = 1.0;
       header.stride(0) = 1;
       header.stride(1) = 2;
       header.stride(2) = 3;

diff --git a/docs/reference/commands/fixelconnectivity.rst b/docs/reference/commands/fixelconnectivity.rst
@@ -39,6 +39,15 @@ Options that influence generation of the connectivity matrix / matrices
 
 -  **-mask file** provide a fixel data file containing a mask of those fixels to be computed; fixels outside the mask will be empty in the output matrix
 
+-  **-tck_weights_in path** specify a text scalar file containing the streamline weights
+
+Options for additional outputs to be generated
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+-  **-count path** export a fixel data file encoding the number of connections for each fixel
+
+-  **-extent path** export a fixel data file encoding the extent of connectivity (sum of weights) for each fixel
+
 Standard options
 ^^^^^^^^^^^^^^^^
 

diff --git a/src/dwi/tractography/weights.h b/src/dwi/tractography/weights.h
@@ -23,7 +23,6 @@ namespace MR
 {
   namespace DWI
   {
-
     namespace Tractography
     {
 

diff --git a/src/fixel/filter/smooth.h b/src/fixel/filter/smooth.h
@@ -18,6 +18,7 @@
 #ifndef __fixel_filter_smooth_h__
 #define __fixel_filter_smooth_h__
 
+#include "fixel/fixel.h"
 #include "fixel/matrix.h"
 #include "fixel/filter/base.h"
 
@@ -51,7 +52,7 @@ namespace MR
        */
 
       class Smooth : public Base
-      { 
+      {
 
         public:
           Smooth (Image<index_type> index_image,