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.
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
if that’s not enough, set the
TmpFileDir config 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
And on the off-chance that this might prove useful to you, we have a tutorial on using the command -line, where the concept of absolute and relative paths is discussed (which should have avoided the confusion about where the folder is…).
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…
Try typing this into your terminal:
echo "TmpFileDir: ." > ~/.mrtrix.conf
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