Dwipreproc command error

1

Dear experts

I have been facing this error for couple of my subjects after running dwipreproc and I was wondering if anyone can help to solve the problem.

Command: applytopup --imain=dwi_pe_1.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pe_1_topup.nii.gz --method=jac
Command: mrconvert dwi_pe_1_topup.nii.gz dwi_pe_1_topup.mif -json_import dwi_pe_1.json
Traceback (most recent call last):
File “/home/luna.kuleuven.be/u0061701/mrtrix3/bin/dwipreproc”, line 488, in
run.command('mrconvert ’ + temp_path + ’ ’ + output_path + ’ -json_import ’ + json_path)
File “/home/luna.kuleuven.be/u0061701/mrtrix3/lib/mrtrix3/run.py”, line 183, in command
stderr_text = tempfiles[index][1].read().decode(‘utf-8’)
File “/usr/lib/python2.7/encodings/utf_8.py”, line 16, in decode
return codecs.utf_8_decode(input, errors, True)
UnicodeDecodeError: ‘utf8’ codec can’t decode byte 0xc9 in position 228: invalid continuation byte

Running the applytopup inside the folder also did not solve the problem.

Thanks and cheers,
Hamed

2

Please ignore. The issue was solved by replacing “Ë” with “E” in the subject’s name of json file. :slight_smile:

Cheers, H

3

Hi Hamed,

This issue is identical to the one already raised on GitHub here. We’ll need to re-raise that issue, and try to decide the best compromise beween development time & robustness of solution. So thanks for posting, and glad you’ve got a quick and easy work-around :+1:

Rob

4

Thanks Rob.
Cheers, -H