Need help with this so much = mrview: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access (prior discussions did not work))

3

Ok, this is unlikely to have anything to do with temporary file storage – as implied in your other (presumably related) thread. It’s also very unlikely to have anything to do with raw memory storage either, since all 3 files will be accessed via memory mapping, and if there were an out-of-memory issue, I’d expect that to lead to the program being killed, without producing a segmentation fault error.

In general, a segmentation fault means some part of our code has tried to access a memory region is does not have access to – either because it is an invalid region, or because it doesn’t permission. This typically means there’s a bug in the code somewhere… But getting to the root of the problem can be difficult – there’s a whole wiki article on how to debug such problems if you have the time.

But before you do that, there are a few things you do to try to isolate the issue:

  • post the output of mrinfo on each of your input files – just so we can see how big they are and whether that might contribute to the issue.

  • run the mrview command with the -debug flag, and copy/paste the full terminal output this produces right up to the crash back on this thread. That should at least give us a hint as to where the program got to before it crashed.

  • try running mrview without command-line arguments, open your sub-01_den_preproc_unbiased.mif image using the File → open menu, then load each overlay image using the Overlay tool, then apply the desired colourmap to each. If that works without crashing, then that will give us a fairly strong hint as to where the problem might be…

  • simplify the command-line until it doesn’t crash:

    • Start by removing one of the -overlay.colourmap N options, then the other, then both.
    • If that still crashes, try also removing one of the -overlay.load image options, then the other, then both.
    • if that still crashes, then you’re left with just a straight mrview sub-01_den_preproc_unbiased.mif, which ought to work according to your post…

Hopefully that process will give us a hint as to where to look in the code for any issues that could cause such a crash…

All the best,
Donald.