Hi Rob,
This seems like a very sensible explanation! Thank you. I was also surprised that eddy ran with --mporder but no slspec.txt file.
I have tried running dwipreproc and specifying the full directory to the slspec.txt however I either get the following error if I include a “/” at the start of the path
Command: eddy_cuda --imain=dwi.nii --mask=mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --repol --mporder=18 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=5 –slspec=/data/users/DSA/EDDYTEST/my_slspec.txt --out=dwi_post_eddy
Traceback (most recent call last):
File “/data/bin/mrtrix3/bin/dwipreproc”, line 518, in
run.command(eddy_cmd + ’ --imain=dwi.nii --mask=mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals’ + eddy_in_topup_option + eddy_manual_options + ’ --out=dwi_post_eddy’)
File “/data/bin/mrtrix3/lib/mrtrix3/run.py”, line 175, in command
stdout_text = tempfiles[index][0].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 0xa0 in position 0: invalid start byte
or the same ‘msg=MultiBandGroups: Unable to open file error’ as before if not including the “/” i.e. –slspec=data/users/DSA/EDDYTEST/my_slspec.txt
Thus, it does not look like I will be able to provide the full path to my slspec.txt file within dwipreproc.
I’m looking forward to the updates you detailed! How imminent are these going to being available? In the meantime do you see a workaround? Is it possible to copy slspec.txt into the dwipreproc temporary directory and ‘restart’ dwipreproc from there?
Thank you again!
Derek