Merge branch 'master' into dev

Author: jdtournier

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