Advanced debuggingΒΆ

On rare occasions, a user may encounter a critical error (e.g. “Segmentation fault”) within an MRtrix3 command that does not give sufficient information to identify the cause of the problem, and that the developers are unable to reproduce. In these cases, we will often ask to be provided with example data that can consistently reproduce the problem in order to localise the issue. An alternative is for the user to perform an initial debugging experiment, and provide us with the resulting information. The instructions for doing so are below.

  1. If required, install gdb; the GNU Debugging Tool (specific instructions for this installation will depend on your operating system)
  2. Make sure you are using the most up-to-date MRtrix3 code! (git pull)
  3. Configure and compile MRtrix3 in debug mode: ./configure -debug -assert debug; ./build debug Note that this compilation will reside alongside your existing MRtrix3 installation, but will not interfere with it in any way. Commands that are compiled in debug mode will reside in the debug/bin directory.
  4. Execute the problematic command within gdb: gdb --args debug/bin/command (arguments) (-options) -debug Note that the version of the command that is compiled in debug mode resides in the debug/bin directory; you must provide this full path explicitly to ensure that this is the version of the command that is executed. The preceding gdb --args at the beginning of the line is simply the easiest way to execute the command within gdb. Include all of the file paths, options etc. that you used previously when the problem occurred. It is also recommended to use the MRtrix3 -debug option so that MRtrix3 produces more verbose information at the command-line.
  5. Once gdb has loaded, type r and hit ENTER to run the command.
  6. If an error is encountered, gdb will print an error, and then provide a terminal with (gdb) shown on the left hand side. Type bt and hit ENTER: This stands for ‘backtrace’, and will print details on the internal code that was running when the problem occurred.
  7. Copy all of the raw text, from the command you ran in instruction 3 all the way down to the bottom of the backtrace details, and send it to us. The best place for these kind of reports is to make a new issue in the Issues tracker for the GitHub repository.
  8. If gdb does not report any error, it is possible that a memory error is occurring, but even the debug version of the software is not performing the necessary checks to detect it. If this is the case, you can also try using Valgrind, which will perform a more exhaustive check for memory faults (and correspondingly, the command will run exceptionally slowly): valgrind debug/bin/command (arguments) (-options)

We greatly appreciate any contribution that the community can make toward making MRtrix3 as robust as possible, so please don’t hesitate to report any issues you encounter.