QSIprep error biascorr

mblesac · January 31, 2022, 2:07pm

Hi,

I’m running QSIprep with the following command:

  export SINGULARITY_TMPDIR=$2/tmp
  export SINGULARITY_CACHEDIR=$2/tmp
  export SINGULARITYENV_TEMPLATEFLOW_HOME=/opt/templateflow


  singularity run --contain --nv -C -B /EBC:/EBC,$2:/opt/templateflow ${QSIprep}/qsiprep-0.14.2.sif $2/BIDs_data $2/derivatives/sub-${NAME}/ses-01/dwi participant --participant-label sub-${NAME} -w $2/${NAME}_QSIprep_working_directory --nthreads 16 --omp-nthreads 16 --denoise-after-combining --fs-license-file /EBC/local/infantFS/freesurfer/license.txt --dwi-denoise-window 7 --unringing-method mrdegibbs --dwi-only --infant --output-resolution 1.25 --eddy-config $2/eddy_params.json --recon-spec reorient_fslstd --stop-on-first-crash --skip_bids_validation #> $2/derivatives/sub-${NAME}/ses-01/dwi/log_QSIprep_sub-${NAME}.txt

And the following error appears:

 [Node] Setting-up "qsiprep_wf.single_subject_8018_wf.dwi_preproc_ses_01_wf.pre_hmc_wf.merge_and_denoise_wf.merged_denoise.biascorr" in "/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr".
220131-13:59:04,274 nipype.workflow INFO:
         [Node] Running "biascorr" ("qsiprep.interfaces.mrtrix.DWIBiasCorrect"), a CommandLine Interface with command:
dwibiascorrect -ants.b [150,3] -ants.c [200x200,1e-6] -bias sub-8018_ses-01_dwi_denoised_mrdegibbs_bias.nii.gz -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval -mask /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz -ants /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz sub-8018_ses-01_dwi_denoised_mrdegibbs_N4.nii.gz
220131-13:59:18,883 nipype.workflow WARNING:
         Storing result file without outputs
220131-13:59:18,886 nipype.workflow WARNING:
         [Node] Error on "qsiprep_wf.single_subject_8018_wf.dwi_preproc_ses_01_wf.pre_hmc_wf.merge_and_denoise_wf.merged_denoise.biascorr" (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr)
220131-13:59:20,151 nipype.workflow ERROR:
         Node biascorr failed to run on host EBC33.
220131-13:59:20,165 nipype.workflow ERROR:
         Saving crash info to /EBC/home/mblesa/QSIprep_neonates/derivatives/sub-8018/ses-01/dwi/qsiprep/sub-8018/log/20220131-125114_ad11c06f-5b65-458e-9a64-40d6b983a8bb/crash-20220131-135920-s1474782-biascorr-c7cf0767-dbe3-4239-9570-7400c4fbc971.txt
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 428, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 753, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
dwibiascorrect -ants.b [150,3] -ants.c [200x200,1e-6] -bias sub-8018_ses-01_dwi_denoised_mrdegibbs_bias.nii.gz -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval -mask /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz -ants /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz sub-8018_ses-01_dwi_denoised_mrdegibbs_N4.nii.gz
Standard output:

Standard error:
dwibiascorrect:
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect:
dwibiascorrect: Generated temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/in.mif -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/mask.mif
dwibiascorrect: Changing to temporary directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/)
Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect:
dwibiascorrect: [ERROR] Command failed: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3 (dwibiascorrect:107)
dwibiascorrect: Output of failed command:
                dwiextract: extracting volumes...  [==============
                dwiextract: [SYSTEM FATAL CODE: SIGBUS (7)] Bus error: Accessing invalid address (out of storage space?)
                mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
                mrmath: [ERROR] error opening image "-"
dwibiascorrect:
dwibiascorrect: Changing back to original directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr)
dwibiascorrect: Script failed while executing the command: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect: For debugging, inspect contents of temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Return code: 1

QSIPrep failed: 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 428, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 753, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
dwibiascorrect -ants.b [150,3] -ants.c [200x200,1e-6] -bias sub-8018_ses-01_dwi_denoised_mrdegibbs_bias.nii.gz -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval -mask /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz -ants /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz sub-8018_ses-01_dwi_denoised_mrdegibbs_N4.nii.gz
Standard output:

Standard error:
dwibiascorrect:
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect:
dwibiascorrect: Generated temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/in.mif -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/mask.mif
dwibiascorrect: Changing to temporary directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/)
Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect:
dwibiascorrect: [ERROR] Command failed: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3 (dwibiascorrect:107)
dwibiascorrect: Output of failed command:
                dwiextract: extracting volumes...  [==============
                dwiextract: [SYSTEM FATAL CODE: SIGBUS (7)] Bus error: Accessing invalid address (out of storage space?)
                mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
                mrmath: [ERROR] error opening image "-"
dwibiascorrect:
dwibiascorrect: Changing back to original directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr)
dwibiascorrect: Script failed while executing the command: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect: For debugging, inspect contents of temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Return code: 1

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/cli/run.py", line 647, in main
    qsiprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 164, in run
    self._clean_queue(jobid, graph, result=result)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
    raise RuntimeError("".join(result["traceback"]))
RuntimeError: 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 428, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 753, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
dwibiascorrect -ants.b [150,3] -ants.c [200x200,1e-6] -bias sub-8018_ses-01_dwi_denoised_mrdegibbs_bias.nii.gz -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval -mask /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz -ants /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz sub-8018_ses-01_dwi_denoised_mrdegibbs_N4.nii.gz
Standard output:

Standard error:
dwibiascorrect:
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect:
dwibiascorrect: Generated temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/degibbser/sub-8018_ses-01_dwi_denoised_mrdegibbs.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/in.mif -fslgrad /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bvec /EBC/home/mblesa/QSIprep_neonates/BIDs_data/sub-8018/ses-01/dwi/sub-8018_ses-01_dwi.bval
Command:  mrconvert /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/quick_mask/sub-8018_ses-01_dwi_denoised_mrdegibbs_b0_series_mask.nii.gz /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/mask.mif
dwibiascorrect: Changing to temporary directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/)
Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect:
dwibiascorrect: [ERROR] Command failed: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3 (dwibiascorrect:107)
dwibiascorrect: Output of failed command:
                dwiextract: extracting volumes...  [==============
                dwiextract: [SYSTEM FATAL CODE: SIGBUS (7)] Bus error: Accessing invalid address (out of storage space?)
                mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
                mrmath: [ERROR] error opening image "-"
dwibiascorrect:
dwibiascorrect: Changing back to original directory (/EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr)
dwibiascorrect: Script failed while executing the command: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
dwibiascorrect: For debugging, inspect contents of temporary directory: /EBC/home/mblesa/QSIprep_neonates/8018_QSIprep_working_directory/qsiprep_wf/single_subject_8018_wf/dwi_preproc_ses_01_wf/pre_hmc_wf/merge_and_denoise_wf/merged_denoise/biascorr/dwibiascorrect-tmp-QB0WLU/
Return code: 1

Sentry is attempting to send 3 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit
INFO:    Cleaning up image...

If I run the command with sudo permissions I can run it, but without sudo this is what happens. Any clue to solve this? Thanks in advance.

Best regards,

Manuel

Steven · January 31, 2022, 2:26pm

I’m guessing it is because your temp space is running out of memory… Is your $2 argument space-limited?

mblesac · January 31, 2022, 2:41pm

Hi,

No, it is the current directory with around 200GB space. It is curious that fails at this step, why the others work fine? it could be related with the default scratch directory used by dwibiascorr (MRtrix)?

Best regards,

Manuel

Steven · January 31, 2022, 2:58pm

Can you try removing the --contain and -C flags? I think those alter how singularity interacts with your local file system.

Also,

You only need to put $s/derivatives for your output argument.

mblesac · January 31, 2022, 3:18pm

Hi,

I removed those flags and I got this error:

INFO:    Converting SIF file to temporary sandbox...
WARNING: underlay of /usr/bin/nvidia-smi required more than 50 (445) bind mounts
WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (95) bind mounts
Traceback (most recent call last):
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/core/__init__.py", line 17, in <module>
    from . import multiarray
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/core/multiarray.py", line 14, in <module>
    from . import overrides
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/cli/run.py", line 546, in main
    from nipype import logging as nlogging
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/nipype/__init__.py", line 18, in <module>
    from .utils.config import NipypeConfig
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/nipype/utils/config.py", line 19, in <module>
    import numpy as np
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/EBC/local/FSL5011/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/core/__init__.py", line 47, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy c-extensions failed.
- Try uninstalling and reinstalling numpy.
- If you have already done that, then:
  1. Check that you expected to use Python3.7 from "/usr/local/miniconda/bin/python",
     and that you have no directories in your PATH or PYTHONPATH that can
     interfere with the Python and numpy version "1.17.4" you're trying to use.
  2. If (1) looks fine, you can open a new issue at
     https://github.com/numpy/numpy/issues.  Please include details on:
     - how you installed Python
     - how you installed numpy
     - your operating system
     - whether or not you have multiple versions of Python installed
     - if you built from source, your compiler versions and ideally a build log

- If you're working with a numpy git repository, try `git clean -xdf`
  (removes all files not under version control) and rebuild numpy.

Note: this error has many possible causes, so please don't comment on
an existing issue about this - open a new one instead.

Original error was: No module named 'numpy.core._multiarray_umath'

INFO:    Cleaning up image...

Now I’m trying with the flag --dwi-no-biascorr. Another doubt I have, why it always creates a sandbox? thanks in advance.

Best regards,

Manuel

mblesac · January 31, 2022, 4:09pm

Hi,

By using --dwi-no-biascorr it doesn’t crash. Any clue what could be happening?

Manuel

Steven · January 31, 2022, 4:22pm

Add the -e flag to singularity run. Singularity is attempting to use FSLpython from your own file system. The -e flag will make sure your environmental variables are not passed into QSIPrep.

mblesac · February 3, 2022, 10:08pm

Hi,

Thanks that works!

Best regards,

Manuel