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Inconsistent bvals and bvecs #82

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dlevitas opened this issue Feb 25, 2020 · 6 comments · Fixed by #100
Closed

Inconsistent bvals and bvecs #82

dlevitas opened this issue Feb 25, 2020 · 6 comments · Fixed by #100
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@oesteban @dPys
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bug Something isn't working effort: low This task does not seem time consuming impact: high This contribution/idea will help a lot of people
Milestone
0.3.0

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@dlevitas
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dlevitas commented Feb 25, 2020 •
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  • dmriprep version: 0.2.2
  • Python version: 3.6.8
  • Operating System: Red Hat Enterprise Linux Server 7.7 (Maipo)

Description

I am getting an error message regarding the bvals and bvecs my data. My dataset is BIDS compliant (per the BIDS online validator; version 1.4.2). This is my first foray into dmriprep, so I'm not really sure how to troubleshoot this issue.

What I Did

I used the following dmriprep singularity command (container created from singularity version 2.6.1):

export SINGULARITYENV_TEMPLATEFLOW_HOME=/N/dcwan/projects/irf/templateflow

unset PYTHONPATH; singularity run -B /N/dcwan/projects/irf/templateflow:/opt/templateflow /N/dcwan/projects/irf/containers/dmriprep-0.2.2.simg \
		$bids_root_dir $bids_root_dir/derivatives						\
		participant														\
		--skip-bids-validation 											\
		--participant-label 01 											\
		--fs-license-file $FREESURFER_HOME/license.txt 					\
		--output-spaces fsaverage:den-10k MNI152NLin6Asym:res-2			\
		--nprocs 8												\
		--stop-on-first-crash 											\
		--resource-monitor 												\
		--low-mem 														\
		--mem_mb 35000 												\
		--use-plugin $bids_root_dir/dmriprep_plugin_01.yml 			\
		--verbose 														\
		-w $bids_root_dir/derivatives

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 585, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 678, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 382, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/interfaces/vectors.py", line 75, in _run_interface
    b0_threshold=self.inputs.b0_threshold,
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 57, in __init__
    self.generate_rasb()
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 141, in generate_rasb
    self.normalize()
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 135, in normalize
    b_scale=self._b_scale)
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 248, in normalize_gradients
    (b0s.sum(), b0_vecs.sum()))
ValueError: Inconsistent bvals and bvecs (5, 0 low-b, respectively).
@oesteban
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I can confirm this replicates with ds001771 (see new smoke test #91). I'll be working on this with you, @dPys - if you'd like.

@oesteban oesteban added the bug Something isn't working label Mar 23, 2020
@oesteban oesteban added this to the 0.3.0 milestone Mar 23, 2020
@oesteban oesteban added impact: high This contribution/idea will help a lot of people effort: low This task does not seem time consuming labels Mar 23, 2020
@oesteban
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This is the error in detail (here and here):

Node: dmriprep_wf.single_subject_36_wf.dwi_preproc_acq_AP_wf.gradient_table
Working directory: /work/dmriprep_wf/single_subject_36_wf/dwi_preproc_acq_AP_wf/gradient_table

Node inputs:

b0_threshold = 50.0
b_scale = True
bvec_norm_epsilon = 0.1
dwi_file = /data/sub-36/dwi/sub-36_acq-AP_dwi.nii.gz
in_bval = /data/sub-36/dwi/sub-36_acq-AP_dwi.bval
in_bvec = /data/sub-36/dwi/sub-36_acq-AP_dwi.bvec
in_rasb = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.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 397, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/interfaces/vectors.py", line 77, in _run_interface
    b0_threshold=self.inputs.b0_threshold,
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 97, in __init__
    self.generate_rasb()
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 183, in generate_rasb
    self.normalize()
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 176, in normalize
    b_scale=self._b_scale,
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/utils/vectors.py", line 334, in normalize_gradients
    (b0s.sum(), b0_vecs.sum()))
ValueError: Inconsistent bvals and bvecs (7, 0 low-b, respectively).

@oesteban oesteban mentioned this issue Mar 24, 2020
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@oesteban
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@dPys

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dPys commented Mar 24, 2020

This should now be resolved with 8b365f8
@oesteban @dlevitas

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Hey @dPys, could we address this in a separate PR?

@dPys
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dPys commented Mar 25, 2020

Sounds good @oesteban . Should I open a new one or add it as a rider to #76 ?

oesteban added a commit to oesteban/dmriprep that referenced this issue Apr 6, 2020
@oesteban
ENH: Do not raise error in all instances of b-vecs/vals inconsistencies
d1b93aa 
We raised a ValueError whenever the number of b-vals and all-zero b-vecs
didn't match. Few lines later, we would overwrite nonzero b-vecs to
match the b-vals, but that step was never reached. This PR allows the
function to just throw a warning instead.

Resolves: nipreps#82
@oesteban oesteban mentioned this issue Apr 6, 2020
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ENH: Do not raise error in all instances of b-vecs/vals inconsistencies oesteban/dmriprep
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@oesteban @dPys @dlevitas