Sudden error with dwi2response

1

Hi

I’m running into a strange error with dwi2response. Note I have attempted to use the config file ScriptScratchDir option and ‘tempfiledir’ option to see if this will help. It was running fine and suddenly I have this error:

dwi2response dhollander PC04.mif -mask mask.mif wm.txt gm.txt csf.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 scratch directory: /Users/home/Documents/mrtrix_temp_file/dwi2response-tmp-PTN849/
dwi2response: Importing DWI data (/Users/home/Desktop/Mrtrix_sample/PC04.mif)…
dwi2response: Importing mask (/Users/home/Desktop/Mrtrix_sample/mask.mif)…
dwi2response: Changing to scratch directory (/Users/home/Documents/mrtrix_temp_file/dwi2response-tmp-PTN849/)
dwi2response: [ERROR] Unhandled Python exception:
dwi2response: [ERROR] AssertionError:
dwi2response: [ERROR] Traceback:
dwi2response: [ERROR] /Users/home/mrtrix3/bin/dwi2response:114 (in execute())
dwi2response: [ERROR] if not image.statistics(‘mask.mif’, mask=‘mask.mif’).count:
dwi2response: [ERROR] /Users/home/mrtrix3/lib/mrtrix3/image.py:251 (in statistics())
dwi2response: [ERROR] assert len(line) == len(IMAGE_STATISTICS)

When I run it with -debug it runs fine until the mrstats portion.

dwi2response: Command: ‘/Users/home/mrtrix3/bin/mrstats mask.mif -output mean -output median -output std -output std_rv -output min -output max -output count -mask mask.mif’ (piping data to local storage)
dwi2response: [ERROR] Unhandled Python exception:
dwi2response: [ERROR] AssertionError:
dwi2response: [ERROR] Traceback:
dwi2response: [ERROR] /Users/home/mrtrix3/bin/dwi2response:114 (in execute())
dwi2response: [ERROR] if not image.statistics(‘mask.mif’, mask=‘mask.mif’).count:
dwi2response: [ERROR] /Users/home/mrtrix3/lib/mrtrix3/image.py:251 (in statistics())
dwi2response: [ERROR] assert len(line) == len(IMAGE_STATISTICS)

I’m a little lost as this error suddenly appeared with no changes. I noticed another post on it that the user said resolved itself. Any input would be greatly appreciated.

Thank You
Patrick

2

This sounds like it might be similar to this issue, which we’ve just pushed a fix for. Assuming you have a source install (not one of the pre-compiled packages), you can update now and see if that resolves the problem, using these instructions:

cd mrtrix3    # or wherever you have installed MRtrix3
git pull
./build

Otherwise, you may need to wait until we push out the next micro release – it’ll be 3.0.2, but I’m not sure what the timelines will be for that one given that we’ve only just pushed out 3.0.1…

3

Hey

Thanks for the response, I ended up just doing a full reinstall of both python and Mrtrix (and a few other things out of frustration). The problem no longer shows up and everything appears to run correctly so hopefully all is well.

Thanks a lot for the reply!

Patrick