Merge branch 'master' into dev

bin/dwifslpreproc

@@ -1203,7 +1203,7 @@ def execute(): #pylint: disable=unused-variable
     # Also grab any files generated by the eddy qc tool QUAD
     if os.path.isdir('dwi_post_eddy.qc'):
       if app.FORCE_OVERWRITE and os.path.exists(os.path.join(eddyqc_path, 'quad')):
-        run.function(shutil.rmtree(os.path.join(eddyqc_path, 'quad')))
+        run.function(shutil.rmtree, os.path.join(eddyqc_path, 'quad'))
       run.function(shutil.copytree, 'dwi_post_eddy.qc', os.path.join(eddyqc_path, 'quad'))
     # Also grab the brain mask that was provided to eddy if -eddyqc_all was specified
     if app.ARGS.eddyqc_all:

cmd/mrconvert.cpp

@@ -63,7 +63,7 @@ void usage ()
   + "The -vox option is used to change the size of the voxels in the output "
     "image as reported in the image header; note however that this does not "
     "re-sample the image based on a new voxel size (that is done using the "
-    "mrresize command)."
+    "mrgrid command)."
 
   + "By default, the intensity scaling parameters in the input image header "
     "are passed through to the output image header when writing to an integer "

cmd/mrthreshold.cpp

@@ -200,8 +200,7 @@ default_type calculate (Image<value_type>& in,
                         const default_type percentile,
                         const ssize_t bottom,
                         const ssize_t top,
-                        const bool ignore_zero,
-                        const bool to_cout)
+                        const bool ignore_zero)
 {
   if (std::isfinite (abs)) {
 
@@ -249,9 +248,6 @@ default_type calculate (Image<value_type>& in,
 
   } else { // No explicit mechanism option: do automatic thresholding
 
-    std::unique_ptr<LogLevelLatch> latch;
-    if (to_cout)
-      latch.reset (new LogLevelLatch (App::log_level - 1));
     if (max_axis < in.ndim()) {
 
       // Need to extract just the current 3D volume
@@ -302,14 +298,8 @@ void apply (Image<value_type>& in,
             const size_t max_axis,
             const value_type threshold,
             const operator_type comp,
-            const bool mask_out,
-            const bool to_cout)
+            const bool mask_out)
 {
-  if (to_cout) {
-    std::cout << threshold;
-    return;
-  }
-
   const T true_value = std::is_floating_point<T>::value ? 1.0 : true;
   const T false_value = std::is_floating_point<T>::value ? NaN : false;
 
@@ -335,7 +325,9 @@ void apply (Image<value_type>& in,
 
 
 
-
+// TODO Don't write directly to std::cout;
+//   will get hidden by /r of progress bar
+// Alternatively, withhold progress bar if writing to std::cout
 template <typename T>
 void execute (Image<value_type>& in,
               Image<bool>& mask,
@@ -363,19 +355,27 @@ void execute (Image<value_type>& in,
 
     // Do one volume at a time
     // If writing to cout, also add a newline between each volume
-    bool is_first_loop = true;
-    for (auto l = Loop("Determining and applying per-volume thresholds", 3, in.ndim()) (in); l; ++l) {
-      if (to_cout) {
+    if (to_cout) {
+      LogLevelLatch latch (App::log_level - 1);
+      bool is_first_loop = true;
+      for (auto l = Loop(3, in.ndim()) (in); l; ++l) {
         if (is_first_loop)
           is_first_loop = false;
         else
           std::cout << "\n";
+        const default_type threshold = calculate (in, mask, 3, abs, percentile, bottom, top, ignore_zero);
+        std::cout << threshold;
       }
-      LogLevelLatch latch (App::log_level - 1);
-      const default_type threshold = calculate (in, mask, 3, abs, percentile, bottom, top, ignore_zero, to_cout);
-      if (out.valid())
+
+    } else {
+
+      for (auto l = Loop("Determining and applying per-volume thresholds", 3, in.ndim()) (in); l; ++l) {
+        LogLevelLatch latch (App::log_level - 1);
+        const default_type threshold = calculate (in, mask, 3, abs, percentile, bottom, top, ignore_zero);
         assign_pos_of (in, 3).to (out);
-      apply (in, mask, out, 3, value_type(threshold), op, mask_out, to_cout);
+        apply (in, mask, out, 3, value_type(threshold), op, mask_out);
+      }
+
     }
 
     return;
@@ -385,8 +385,11 @@ void execute (Image<value_type>& in,
   }
 
   // Process whole input image as a single block
-  const default_type threshold = calculate (in, mask, in.ndim(), abs, percentile, bottom, top, ignore_zero, to_cout);
-  apply (in, mask, out, in.ndim(), value_type(threshold), op, mask_out, to_cout);
+  const default_type threshold = calculate (in, mask, in.ndim(), abs, percentile, bottom, top, ignore_zero);
+  if (to_cout)
+    std::cout << threshold;
+  else
+    apply (in, mask, out, in.ndim(), value_type(threshold), op, mask_out);
 
 }
 

core/dwi/gradient.cpp

@@ -288,7 +288,8 @@ namespace MR
         // write the scheme as interpreted back into the header if:
         // - vector normalisation effect is large, regardless of whether or not b-value scaling was applied
         // - gradient information was pulled from file
-        if (exceeds_single_precision || get_options ("grad").size() || get_options ("fslgrad").size())
+        // - explicit b-value scaling is requested
+        if (exceeds_single_precision || get_options ("grad").size() || get_options ("fslgrad").size() || bvalue_scaling != BValueScalingBehaviour::Auto)
           set_DW_scheme (const_cast<Header&> (header), grad);
 
         INFO ("found " + str (grad.rows()) + "x" + str (grad.cols()) + " diffusion gradient table");

docs/fixel_based_analysis/mt_fibre_density_cross-section.rst

@@ -64,7 +64,7 @@ There is however no strict requirement for the final set of response functions t
 ^^^^^^^^^^^^^^^^^^^^^^^
 Upsampling DWI data *before* computing FODs increases anatomical contrast and improves downstream template building, registration, tractography and statistics. We recommend upsampling to an isotropic voxel size of 1.25 mm for human brains (if your original resolution is already higher, you can skip this step)::
 
-    for_each * : mrresize IN/dwi_denoised_unringed_preproc_unbiased.mif -vox 1.25 IN/dwi_denoised_unringed_preproc_unbiased_upsampled.mif
+    for_each * : mrgrid IN/dwi_denoised_unringed_preproc_unbiased.mif regrid -vox 1.25 IN/dwi_denoised_unringed_preproc_unbiased_upsampled.mif
 
 
 6. Compute upsampled brain mask images

docs/fixel_based_analysis/st_fibre_density_cross-section.rst

@@ -107,7 +107,7 @@ There is however no strict requirement for the (one) final response function to
 ^^^^^^^^^^^^^^^^^^^^^^^
 Upsampling DWI data *before* computing FODs can increase anatomical contrast and improve downstream template building, registration, tractography and statistics. We recommend upsampling to an isotropic voxel size of 1.25 mm for human brains (if your original resolution is already higher, you can skip this step)::
 
-    for_each * : mrresize IN/dwi_denoised_unringed_preproc_unbiased_normalised.mif -vox 1.25 IN/dwi_denoised_unringed_preproc_unbiased_normalised_upsampled.mif
+    for_each * : mrgrid IN/dwi_denoised_unringed_preproc_unbiased_normalised.mif regrid -vox 1.25 IN/dwi_denoised_unringed_preproc_unbiased_normalised_upsampled.mif
 
 8. Compute upsampled brain mask images
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/quantitative_structural_connectivity/ismrm_hcp_tutorial.rst

@@ -161,7 +161,7 @@ image and provide this alternative FOD image to SIFT (this should have
 little influence on the outcome of the algorithm, but will greatly
 reduce memory consumption):
 
-``mrresize WM_FODs.mif FOD_downsampled.mif -scale 0.5 -interp sinc``
+``mrgrid WM_FODs.mif regrid FOD_downsampled.mif -scale 0.5 -interp sinc``
 
 If this still does not adequately reduce RAM usage, you will need to
 reduce the number of input streamlines to a level where your processing

docs/reference/commands/mrconvert.rst

@@ -27,7 +27,7 @@ Note that for both the -coord and -axes options, indexing starts from 0 rather t
 
 Additionally, for the second input to the -coord option and the -axes option, you can use any valid number sequence in the selection, as well as the 'end' keyword (see the main documentation for details); this can be particularly useful to select multiple coordinates.
 
-The -vox option is used to change the size of the voxels in the output image as reported in the image header; note however that this does not re-sample the image based on a new voxel size (that is done using the mrresize command).
+The -vox option is used to change the size of the voxels in the output image as reported in the image header; note however that this does not re-sample the image based on a new voxel size (that is done using the mrgrid command).
 
 By default, the intensity scaling parameters in the input image header are passed through to the output image header when writing to an integer image, and reset to 0,1 (i.e. no scaling) for floating-point and binary images. Note that the -scaling option will therefore have no effect for floating-point or binary output images.
 

matlab/write_mrtrix.m

@@ -142,9 +142,9 @@ function write_mrtrix (image, filename)
 
 if strcmp(filename(end-3:end), '.mif')
   dataoffset = ftell (fid) + 18;
-  dataoffset += mod((4 - mod(dataoffset, 4)), 4);
+  dataoffset = dataoffset + mod((4 - mod(dataoffset, 4)), 4);
   fprintf (fid, '. %d\nEND\n              ', dataoffset);
-  fseek (fid, dataoffset);
+  fseek (fid, dataoffset, 'bof');
 elseif strcmp(filename(end-3:end), '.mih')
   datafile = [ filename(1:end-4) '.dat' ];
   fprintf (fid, '%s 0\nEND\n', datafile);

run_tests

@@ -82,13 +82,17 @@ EOD
 
 
 if [ ! -z $datadir ]; then
-  echo -n "fetching requisite test data... "
+  echo -n "checking for requisite test data... "
   git submodule update --init $datadir >> $LOGFILE 2>&1
   if [ $? != 0 ]; then
-    echo ERROR!
-    exit 1
+    if [[ -e $datadir && ! -z $(ls -A $datadir) ]]; then
+      echo "Found; UNABLE TO VERIFY VERSION MATCH"
+    else
+      echo "ERROR!"
+      exit 1
+    fi
   else
-    echo OK
+    echo "Synchronized OK"
   fi
 fi
 

share/mrtrix3/labelconvert/fs2lobes_cinginc_convert.txt

@@ -58,6 +58,7 @@
 
 5     Left-Cerebellum-Cortex
 
+6     Left-Thalamus
 6     Left-Thalamus-Proper
 6     Left-Caudate
 6     Left-Putamen
@@ -66,6 +67,7 @@
 6     Left-Amygdala
 6     Left-Accumbens-area
 
+7     Right-Thalamus
 7     Right-Thalamus-Proper
 7     Right-Caudate
 7     Right-Putamen

share/mrtrix3/labelconvert/fs2lobes_cingsep_convert.txt

@@ -58,6 +58,7 @@
 
 6     Left-Cerebellum-Cortex
 
+7     Left-Thalamus
 7     Left-Thalamus-Proper
 7     Left-Caudate
 7     Left-Putamen
@@ -66,6 +67,7 @@
 7     Left-Amygdala
 7     Left-Accumbens-area
 
+8     Right-Thalamus
 8     Right-Thalamus-Proper
 8     Right-Caudate
 8     Right-Putamen

share/mrtrix3/labelconvert/fs_a2009s.txt

@@ -94,6 +94,7 @@
 
 75     Left-Cerebellum-Cortex           230 148 34  255
 
+76     Left-Thalamus                    0   118 14  255
 76     Left-Thalamus-Proper             0   118 14  255
 77     Left-Caudate                     122 186 220 255
 78     Left-Putamen                     236 13  176 255
@@ -102,6 +103,7 @@
 81     Left-Amygdala                    103 255 255 255
 82     Left-Accumbens-area              255 165 0   255
 
+83     Right-Thalamus                   0   118 14  255
 83     Right-Thalamus-Proper            0   118 14  255
 84     Right-Caudate                    122 186 220 255
 85     Right-Putamen                    236 13  176 255

share/mrtrix3/labelconvert/fs_default.txt

@@ -54,6 +54,7 @@
 
 35    L.CER   Left-Cerebellum-Cortex          230 148 34  255
 
+36    L.TH    Left-Thalamus                   0   118 14  255
 36    L.TH    Left-Thalamus-Proper            0   118 14  255
 37    L.CA    Left-Caudate                    122 186 220 255
 38    L.PU    Left-Putamen                    236 13  176 255
@@ -62,6 +63,7 @@
 41    L.AM    Left-Amygdala                   103 255 255 255
 42    L.AC    Left-Accumbens-area             255 165 0   255
 
+43    R.TH    Right-Thalamus                  0   118 14  255
 43    R.TH    Right-Thalamus-Proper           0   118 14  255
 44    R.CA    Right-Caudate                   122 186 220 255
 45    R.PU    Right-Putamen                   236 13  176 255

src/gui/mrview/tool/connectome/connectome.cpp

@@ -2268,6 +2268,8 @@ namespace MR
           for (node_t n = 1; n <= max_index; ++n)
             node_coms[n] *= (1.0f / float(node_volumes[n]));
 
+          selected_nodes.resize (max_index+1);
+
           nodes.clear();
           const size_t pixheight = dynamic_cast<Node_list*>(node_list->tool)->row_height();
 
@@ -2317,8 +2319,6 @@ namespace MR
           node_overlay.reset (new NodeOverlay (std::move (H_overlay)));
           update_node_overlay();
 
-          selected_nodes.resize (num_nodes()+1);
-
           dynamic_cast<Node_list*>(node_list->tool)->initialize();
         }
 
@@ -2755,14 +2755,45 @@ namespace MR
           } else {
             // Load the node names from the LUT
             // Other properties will only be pulled from the LUT if requested
+            // Permit two indices to have a duplicate entry without warning
+            //   (so that using new FreeSurfer tables will not raise a warning);
+            //   if more than two node indices has a duplicate entry, issue the
+            //   user with a warning, as they may have selected the incorrect
+            //   LUT file
+            for (node_t node_index = 1; node_index <= num_nodes(); ++node_index)
+              nodes[node_index].set_name ("");
+            size_t duplicate_entry_count = 0;
             for (node_t node_index = 1; node_index <= num_nodes(); ++node_index) {
               const size_t count = lut.count (node_index);
-              if (count) {
-                if (count > 1)
-                  throw Exception ("Duplicate entries in lookup table file for index " + str(node_index));
+              if (count == 1) {
                 nodes[node_index].set_name (lut.find(node_index)->second.get_name());
+              } else if (count > 1) {
+                ++duplicate_entry_count;
+                vector<std::string> names;
+                const auto range = lut.equal_range (node_index);
+                for (auto i = range.first; i != range.second; ++i)
+                  names.push_back (i->second.get_name());
+                std::nth_element (names.begin(), names.begin(), names.end());
+                nodes[node_index].set_name (names.front());
+              }
+            }
+            if (duplicate_entry_count > 2) {
+              WARN("Lookup table file contains " + str(duplicate_entry_count) + " indices with duplicate entries; "
+                   "file may be intended for use in conversion rather than visualisation");
+            }
+            size_t absent_entry_count = 0;
+            for (node_t node_index = 1; node_index <= num_nodes(); ++node_index) {
+              if (nodes[node_index].get_volume() && !nodes[node_index].get_name().size()) {
+                const std::string name = "Node " + str(node_index);
+                nodes[node_index].set_name (name);
+                lut.insert (std::make_pair (node_index, MR::Connectome::LUT_node (name)));
+                ++absent_entry_count;
               }
             }
+            if (absent_entry_count) {
+              WARN(str(absent_entry_count) + " indices present in parcellation image with no entry in lookup table; "
+                   "lookup table file and parcellation image may not match");
+            }
           }
 
           calculate_node_visibility();

src/gui/mrview/tool/tractography/track_scalar_file.cpp

@@ -180,24 +180,6 @@ namespace MR
             min_entry->setValue (tractogram->scaling_min());
             max_entry->setValue (tractogram->scaling_max());
 
-            threshold_lower_box->setEnabled (true);
-            if (tractogram->use_discard_lower()) {
-              threshold_lower_box->setChecked(true);
-              threshold_lower->setEnabled (true);
-            } else {
-              threshold_lower->setEnabled (false);
-              threshold_lower_box->setChecked(false);
-            }
-            threshold_upper_box->setEnabled (true);
-            if (tractogram->use_discard_upper()) {
-              threshold_upper_box->setChecked (true);
-              threshold_upper->setEnabled (true);
-            } else {
-              threshold_upper->setEnabled (false);
-              threshold_upper_box->setChecked (false);
-            }
-            threshold_lower->setRate (tractogram->scaling_rate());
-
             colourmap_menu->setEnabled (true);
             colourmap_actions[tractogram->colourmap]->setChecked (true);
             show_colour_bar->setChecked (tractogram->show_colour_bar);
@@ -242,9 +224,9 @@ namespace MR
             threshold_lower    ->setEnabled (tractogram->use_discard_lower());
             threshold_upper_box->setChecked (tractogram->use_discard_upper());
             threshold_upper    ->setEnabled (tractogram->use_discard_upper());
-            threshold_lower->setRate  (tractogram->scaling_rate());
+            threshold_lower->setRate  (tractogram->get_threshold_rate());
             threshold_lower->setValue (tractogram->lessthan);
-            threshold_upper->setRate  (tractogram->scaling_rate());
+            threshold_upper->setRate  (tractogram->get_threshold_rate());
             threshold_upper->setValue (tractogram->greaterthan);
           }
         }

src/gui/mrview/tool/tractography/tractogram.cpp

@@ -520,12 +520,12 @@ namespace MR
                 case TrackColourType::Ends:
                   gl::BindBuffer (gl::ARRAY_BUFFER, colour_buffers[buf]);
                   gl::EnableVertexAttribArray (3);
-                  gl::VertexAttribPointer (3, 3, gl::FLOAT, gl::FALSE_, 3 * sample_stride * sizeof(float), (void*)0);
+                  gl::VertexAttribPointer (3, 3, gl::FLOAT, gl::FALSE_, 3 * sample_stride * sizeof(float), (void*)(3*sample_stride*sizeof(float)));
                   break;
                 case TrackColourType::ScalarFile:
                   gl::BindBuffer (gl::ARRAY_BUFFER, intensity_scalar_buffers[buf]);
                   gl::EnableVertexAttribArray (3);
-                  gl::VertexAttribPointer (3, 1, gl::FLOAT, gl::FALSE_, sample_stride * sizeof(float), (void*)0);
+                  gl::VertexAttribPointer (3, 1, gl::FLOAT, gl::FALSE_, sample_stride * sizeof(float), (void*)(sample_stride*sizeof(float)));
                   break;
                 default:
                   break;
@@ -534,7 +534,7 @@ namespace MR
               if (threshold_type == TrackThresholdType::SeparateFile) {
                 gl::BindBuffer (gl::ARRAY_BUFFER, threshold_scalar_buffers[buf]);
                 gl::EnableVertexAttribArray (4);
-                gl::VertexAttribPointer (4, 1, gl::FLOAT, gl::FALSE_, sample_stride * sizeof(float), (void*)0);
+                gl::VertexAttribPointer (4, 1, gl::FLOAT, gl::FALSE_, sample_stride * sizeof(float), (void*)(sample_stride*sizeof(float)));
               }
 
               gl::BindBuffer (gl::ARRAY_BUFFER, vertex_buffers[buf]);
@@ -811,7 +811,7 @@ namespace MR
             while (file (tck_scalar)) {
 
               const size_t tck_size = tck_scalar.size();
-              assert (tck_size == size_t(original_track_sizes[intensity_scalar_buffers.size()][tck_count]));
+              assert (tck_size == size_t(original_track_sizes[threshold_scalar_buffers.size()][tck_count]));
 
               if (!tck_size)
                 continue;