Merge pull request #653 from MRtrix3/tag_0.3.15

Tag 0.3.15

.travis.yml

@@ -28,4 +28,5 @@ script:
 after_failure: 
   - cat configure.log
   - cat build.log
-  - cat testing/testing.log
+  - cat testing.log
+  - sleep 10

build

@@ -236,6 +236,14 @@ The special target 'doc' is used to update the command documentation, so that
 any modifications to the inline documentation in commands can be propagate
 through to the user documentation site.
 
+By default, 'build' will use all available cores to run a parallel build. In some
+instances, this can cause problems (notably out of RAM errors). You can control 
+how many jobs 'build' will run concurrently using the NUMBER_OF_PROCESSORS 
+environment variable. For example:
+
+  $ NUMBER_OF_PROCESSORS=1 ./build
+
+
 OPTIONS:
 
   -verbose               print each command as it is being invoked

cmd/5tt2gmwmi.cpp

@@ -42,7 +42,7 @@ using namespace App;
 void usage ()
 {
 
-  AUTHOR = "Robert E. Smith (r.smith@brain.org.au)";
+  AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
 
   DESCRIPTION
     + "Generate a mask image appropriate for seeding streamlines on the grey matter - white matter interface";

cmd/5tt2vis.cpp

@@ -41,7 +41,7 @@ using namespace App;
 void usage ()
 {
 
-	AUTHOR = "Robert E. Smith (r.smith@brain.org.au)";
+  AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
 
   DESCRIPTION
   + "generate an image for visualisation purposes from an ACT 5TT segmented anatomical image";

cmd/5ttedit.cpp

@@ -34,7 +34,7 @@ using namespace App;
 void usage ()
 {
 
-	AUTHOR = "Robert E. Smith (r.smith@brain.org.au)";
+  AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
 
   DESCRIPTION
   + "manually set the partial volume fractions in an ACT five-tissue-type (5TT) image using mask images";

cmd/amp2sh.cpp

@@ -28,6 +28,8 @@ using namespace App;
 
 void usage ()
 {
+  AUTHOR = "J-Donald Tournier ([email protected])";
+
   DESCRIPTION
   + "convert a set of amplitudes (defined along a set of corresponding directions) "
     "to their spherical harmonic representation. The spherical harmonic decomposition is "

cmd/connectome2tck.cpp

@@ -87,7 +87,7 @@ void usage ()
 
 
 
-  AUTHOR = "Robert E. Smith (r.smith@brain.org.au)";
+  AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
 
   DESCRIPTION
   + "extract streamlines from a tractogram based on their assignment to parcellated nodes";

cmd/dcmedit.cpp

@@ -28,6 +28,8 @@ using namespace App;
 
 void usage ()
 {
+  AUTHOR = "J-Donald Tournier ([email protected])";
+
   DESCRIPTION
   + "Edit DICOM file in-place. Note that this simply replaces the existing "
     "values without modifying the DICOM structure in any way. Replacement text "

cmd/dcminfo.cpp

@@ -27,6 +27,8 @@ using namespace App;
 
 void usage ()
 {
+  AUTHOR = "J-Donald Tournier ([email protected])";
+
   DESCRIPTION
   + "output DICOM fields in human-readable format.";
 

cmd/dirflip.cpp

@@ -28,7 +28,9 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+  AUTHOR = "J-Donald Tournier ([email protected])";
 
   DESCRIPTION
     + "optimise the polarity of the directions in a scheme with respect to a "

cmd/dirgen.cpp

@@ -28,7 +28,10 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+
+AUTHOR = "J-Donald Tournier ([email protected])";
 
 DESCRIPTION
   + "generate a set of uniformly distributed directions using a bipolar electrostatic repulsion model.";

cmd/dirmerge.cpp

@@ -27,7 +27,9 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+AUTHOR = "J-Donald Tournier ([email protected])";
 
 DESCRIPTION
   + "splice or merge sets of directions over multiple shells into a single set, "

cmd/dirorder.cpp

@@ -26,7 +26,9 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+  AUTHOR = "J-Donald Tournier ([email protected])";
 
   DESCRIPTION
     + "reorder a set of directions to ensure near-uniformity upon truncation - "

cmd/dirsplit.cpp

@@ -27,7 +27,9 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+AUTHOR = "J-Donald Tournier ([email protected])";
 
 DESCRIPTION
   + "split a set of evenly distributed directions (as generated "

cmd/dirstat.cpp

@@ -24,7 +24,9 @@
 using namespace MR;
 using namespace App;
 
-void usage () {
+void usage ()
+{
+  AUTHOR = "J-Donald Tournier ([email protected])";
 
   DESCRIPTION
     + "report statistics on a direction set";

cmd/dwi2adc.cpp

@@ -29,6 +29,8 @@ using namespace std;
 
 void usage ()
 {
+  AUTHOR = "J-Donald Tournier ([email protected])";
+
   DESCRIPTION 
     + "convert mean dwi (trace-weighted) images to mean adc maps";