Error response function

1

Dear all,

I’m running the script dwi2response and I get and error, but I don’t know what it fails.

dwi2response tournier 7101.mif 7101_response.txt

dwi2response: 
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response: 
dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-NIB609/
Command: mrconvert /media/manuel/6abbdb9a-052b-4aa4-9335-dd6bdc507d9f/bmanuel/TRACTOGRAPHY/RAW-DATA/DIFF/7101.mif - -stride 0,0,0,1 | dwiextract - /tmp/dwi2response-tmp-NIB609/dwi.mif
dwi2response: 
dwi2response: [ERROR] Command failed: mrconvert /media/manuel/6abbdb9a-052b-4aa4-9335-dd6bdc507d9f/bmanuel/TRACTOGRAPHY/RAW-DATA/DIFF/7101.mif - -stride 0,0,0,1 | dwiextract - /tmp/dwi2response-tmp-NIB609/dwi.mif
dwi2response: Output of failed command:
dwi2response: Changing back to original directory (/media/manuel/6abbdb9a-052b-4aa4-9335-dd6bdc507d9f/bmanuel/TRACTOGRAPHY/RAW-DATA/DIFF)
dwi2response: Deleting temporary directory /tmp/dwi2response-tmp-NIB609/

Any clue? Thanks in advance

Regards,

Manuel

2

Hi @mblesac,

Could you copy-paste and run this line, and tell us what the output is?

mrconvert /media/manuel/6abbdb9a-052b-4aa4-9335-dd6bdc507d9f/bmanuel/TRACTOGRAPHY/RAW-DATA/DIFF/7101.mif - -stride 0,0,0,1 | dwiextract - test.mif

That should give you / us some insight into what the actual problem is at that very first step of the script!

3

I’d be suspecting an out of RAM problem, similar to this thread. How big is your image? How much RAM do you have on the system? And how much space in /tmp?

4

I think that’s right, is some memory issue, because when I run mrconvert it works without any problem.

My images are 4GB, in /tmp I have 11.8 (I think here is the problem) and the RAM is 66GB

5

That was the problem, I changed the output directory to another hard drive and now works perfect. Thanks!

1 Like
6

Good to know!

I did a little more digging, since I was curious as to why both here and in another thread the script isn’t capturing any of the terminal output from the unsuccessful command:

dwi2response: Output of failed command:
tumbleweed appears on terminal
:disappointed:

The problem is that when the fatal error occurs, the relevant (non-MRtrix3) library doesn’t write the error to the command’s standard error output, but to the current tty terminal. As a result, due to the mechanism used by the Python script library for calling these commands, the script library fails to capture this text, leaving you with an empty error message and a confused look. (Mind you, even if it were printed, the error message itself isn’t that clear: ‘Bus Error (core dumped)’)

I’m trying to fix this so that the script can give a more informative error; but for now, if “Output of failed command” is empty, there’s a good chance that you’ve run out of memory.

Rob