Hi there!
I’m running into this error at the dwi2response step:
dwi2response: Output of failed command:
mrconvert: copying from "/media/nir...en/Tumour/PSychTest/dwi.mif" to "/tmp/mrtrix-tmp-JLYWDl.mif"... [
mrconvert: [SYSTEM FATAL CODE: SIGBUS (7)] Bus error: Accessing invalid address (out of storage space?)
dwiextract: [ERROR] no filename supplied to standard input (broken pipe?)
dwiextract: [ERROR] error opening image "-"
I think I need to make some changes temporary folders so I don’t run out of space, but I’m not sure how to do this - I’m not very experienced with coding.
Any help would be greatly appreciated!!
This looks like a case of running out of space on the /tmp due to the way Unix piping is handled in MRtrix3. Lots of detail on how to handle this on this thread.
Basic summary:
clear out any temporary files from the /tmp folder that might have been left around after previous command crashes or interruptions. These start with the prefix mrtrix-tmp-.
if that’s not enough, set the TmpFileDirconfig file option to point to a location with more storage. The current folder might be simplest, which you can set like this:
Thanks very much for the reply!
I may be looking in the wrong place, but when i look under /mrtrix3/tmp there are no files, only 3 more directories: cmd core and src. So I don’t think it’s due to the temporary files.
Where do I find this config file option? I found a script called config, but it doesn’t have any TmpFileDir lines within it
No, the folder I’m talking about here is the /tmp folder, it’s not within the MRtrix3 folder, but on your system – it’s the default location for temporary files. Have a look with ls /tmp and navigate into it with cd /tmp.
Thank you. That tutorial looks very helpful and I will use it for sure. Also, thanks, I’ve cleared out mp /tmp folder but the issue still remains. Could you give me idiot-proof way to set the TmpFileDir config file option to point somewhere else? Completely clueless regarding how to do this…
Thanks!
Hoping to in the future have a more convenient solution for cleaning up old MRtrix3 files; but given systems can also get bloated by non-MRtrix3 content, it’s worthwhile having an understanding of this stuff anyway
I’m a bit confused here, the command you’re having trouble with looks identical to that in your other thread, but the error message in that other thread was a segmentation fault (SIGSEGV), whereas this one is a bus error (SIGBUS). Is this a typo? Or are you genuinely finding that the same command sometimes produces a bus error, and sometimes a segmentation fault? If that’s the case, then that strongly suggests an issue with the operating system and/or drivers – most likely the drivers for the graphics card (assuming you don’t have any other issues with the command-line tools). I’m assuming you’re running on WSL2, it may be worth applying all system updates on the Windows side and all available updates on the Linux side too…
If that doesn’t fix it, please go through the steps I suggested in response to your other thread, and we’ll see if we can figure it out.
I am trying to fix this issue since last day, I might have updated the error message by trying to fix. I did not notice it is changed untill you pointed it out.
