QSIprep NodeExecutionError: Exception raised while executing Node eddy

[Joseph_Hong]

Hello, everyone!

I am trying to run qsiprep==0.15.2 on our lab server.
However, I got a error with the next comment and crash.txt.

220516-15:54:01,445 nipype.workflow ERROR:
	 Saving crash info to /out/qsiprep/sub-143325/log/20220516-120326_e31e9bd3-ed0a-41b4-a030-083a0fb9662d/crash-20220516-155401-root-eddy-8e847462-0e45-4583-bd64-4e1614dba09d.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'out_parameter' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' for output 'out_parameter' of a ExtendedEddy interface


QSIPrep failed: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'out_parameter' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' for output 'out_parameter' of a ExtendedEddy interface


Traceback (most recent call last):
  File "/usr/local/miniconda/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 659, in main
    qsiprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
    self._clean_queue(jobid, graph, result=result)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 244, in _clean_queue
    raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'out_parameter' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' for output 'out_parameter' of a ExtendedEddy interface

-------------------------------------------------------------------------------------------------------------------------------------
Crash is

Node: qsiprep_wf.single_subject_143325_wf.dwi_preproc_wf.hmc_sdc_wf.eddy
Working directory: /tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy

Node inputs:

args = 
cnr_maps = True
dont_peas = False
dont_sep_offs_move = False
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ', 'OMP_NUM_THREADS': '8'}
estimate_move_by_susceptibility = <undefined>
fep = False
field = <undefined>
field_mat = <undefined>
flm = linear
fudge_factor = 10.0
fwhm = <undefined>
in_acqp = <undefined>
in_bval = <undefined>
in_bvec = <undefined>
in_file = <undefined>
in_index = <undefined>
in_mask = <undefined>
in_topup_fieldcoef = <undefined>
in_topup_movpar = <undefined>
initrand = <undefined>
interp = spline
is_shelled = True
json = <undefined>
mbs_ksp = <undefined>
mbs_lambda = <undefined>
mbs_niter = <undefined>
method = jac
mporder = <undefined>
multiband_factor = <undefined>
multiband_offset = <undefined>
niter = 5
num_threads = 8
nvoxhp = 1000
out_base = eddy_corrected
outlier_nstd = <undefined>
outlier_nvox = <undefined>
outlier_pos = <undefined>
outlier_sqr = <undefined>
outlier_type = <undefined>
output_type = NIFTI_GZ
repol = True
residuals = False
session = <undefined>
slice2vol_interp = <undefined>
slice2vol_lambda = <undefined>
slice2vol_niter = <undefined>
slice_order = <undefined>
slm = linear
use_cuda = True

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'out_parameter' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/qsiprep_wf/single_subject_143325_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_parameters' for output 'out_parameter' of a ExtendedEddy interface

my command was

sudo docker run -it --rm --runtime=nvidia -v /local_raid1/03_user/sunghyoung/01_project/01_qsiprep/02_data:/data:ro -v /local_raid1/03_user/sunghyoung/01_project/01_qsiprep/03_result:/out -v /local_raid1/03_user/sunghyoung/01_project/01_qsiprep/01_software:/software pennbbl/qsiprep /data /out participant --output-resolution 1.2 --eddy-config /software/eddy_params.json --fs-license-file /software/license.txt --nthreads 15

There was same error

Qsiprep: Node eddy failed to run on host sms

Hi everyone! I am trying to run qsiprep==0.15.1 on my cluster server, but qsiprep returns an error during the processing. I run qsiprep with the next command: module load singularity singularity run --cleanenv ~/qsiprep-0.15.1.sif ~/Entropy/raw_data/patients/ ~/Entropy/derivatives_qsiprep/patients/ participant --participant-label OAS30001 -w ~/Entropy/work_qsiprep/patients/ --fs-license-file ~/freesurfer_license.txt --skip_bids_validation --output-resolution 1.2 And at some point it shows an…

Qsiprep processing of HCP S1200 subject

Dear fellow researchers: I’m trying to run qsiprep on a HCP S1200 subject and is running into errors with the eddy processing step. I am running the processing on the raw data after converting it to BIDS format. (I could start from the minimum preprocessed version if there is now a suggested way with qsiprep.) This post maybe similar to some earlier posts, but I did not find a solution. The command that I ran is: singularity run --cleanenv /home/simg/qsiprep-v0.15.3.simg /home/hcp_unprocessed…

The topics are about singularity, but my case is about docker.

Any comments are helpful for me!
Thanks.

[Steven]

Hello, it would help if you could provide the e following information:

1. are your data bids valid? (If not, try to make them bids valid)
2. is this error subject specific or across all subjects?
3. can you specify and bind a working directory? This is the -w argument in qsiprep, which should be bound using the -v flag in Docker.
4. what kind of acquisition are you working with? DTI, HARDI, DSI, or something else?
5. what’s in your Eddy config file? Is there a reason you’re not using the defaults?

Best,
Steven

[Joseph_Hong]

Hello, Steven!
Thanks for your response.

1. My data have three bids validator’s errors (1. volume_count_mismatch 2. bvec_row_length, 3. b_file), however, the files don’t have any problems and from what I experienced they are worked well.

2. It seems to be an error across all subjects, considering that the error has occurred except for the subject where the error occurred initially.

4. I’m going to do the same preprocessing process for the same subject and then try famous and different acquisitions such as DTI, HARDI, and DSI.

5. My eddy config file is based on qsiprep/eddy_params.json at master · PennLINC/qsiprep · GitHub
and I only changed “use_cuda” to use gpu.

3. When I bound a working directory using only one subject, it was solved.

Is this really a problem because there was no working directory?

Best,
Joseph