Out of storage space?

#1

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!!

Unix /tmp becomes full
#2

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 TmpFileDir config file option to point to a location with more storage. The current folder might be simplest, which you can set like this:

    TmpFileDir: .
#3

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

#4

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.

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…).

#5

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!

#6

Try typing this into your terminal:

echo "TmpFileDir: ." > ~/.mrtrix.conf
#7

success! Many thanks.

#8

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 :+1: