Gradient files not matching after rotation (macaque DWI)

[smeisler]

Hello,

Installation

QSIPrep 0.14.2 running on Linux HPC via Singularity

Bug description

Referring #292 . I have macaque DWI/T1 images that have the wrong orientation labels in visualization software (e.g. fslview). I rotated them with MRIcroMtl to correct the labels, and exported new bval/vecs using MrTrix3 dwigradcheck. I tried to QSIPrep (infant mode, dwi only), and got an error:

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py", line 61, in _run_interface
newpath=runtime.cwd,
File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py", line 171, in _gather_confounds
raise Exception("Gradients or original files don't match. File a bug report!")
Exception: Gradients or original files don't match. File a bug report!

HTML outputs are created, as well as the preprocessed image, but no QC metrics or eddy CNR images are saved out. When using the non-rotated original images, QSIPrep goes to completion.

Also the brain mask is all 1s in both cases, but that's probably due to being in infant mode.

[mattcieslak]

This may work now, please reopen if there are still problems