Hi everyone,
QSIPrep gives this error to me, I wonder about that but I think that refers to input data and JSON file information. I would appreciate it if you could help me. I also attached JSON file.
sub-2001_ses-baseline_run-1_dwi.txt (2.0 KB)
220928-08:59:13,497 nipype.workflow INFO:
[Node] Setting-up "qsiprep_wf.single_subject_2001_wf.dwi_finalize_ses_baseline_wf.transform_dwis_t1.cnr_image_type" in "/flywheel/v0/work/qsiprep_wf/single_subject_2001_wf/dwi_finalize_ses_baseline_wf/transform_dwis_t1/cnr_image_type".
220928-08:59:13,498 nipype.workflow INFO:
[Node] Finished "fdisp", elapsed time 0.003251s.
220928-08:59:13,499 nipype.workflow INFO:
[Node] Finished "add_motion_headers", elapsed time 0.003998s.
220928-08:59:13,501 nipype.workflow INFO:
[Job 98] Completed (qsiprep_wf.single_subject_2001_wf.dwi_preproc_ses_baseline_wf.confounds_wf.add_motion_headers).
220928-08:59:13,502 nipype.workflow INFO:
[Node] Executing "cnr_image_type" <qsiprep.interfaces.ants.GetImageType>
220928-08:59:13,580 nipype.workflow INFO:
[Node] Finished "cnr_image_type", elapsed time 0.076561s.
220928-08:59:15,357 nipype.workflow INFO:
[Job 96] Completed (qsiprep_wf.single_subject_2001_wf.dwi_finalize_ses_baseline_wf.transform_dwis_t1.cnr_image_type).
220928-08:59:15,358 nipype.workflow INFO:
[Job 97] Completed (qsiprep_wf.single_subject_2001_wf.dwi_preproc_ses_baseline_wf.confounds_wf.fdisp).
220928-08:59:15,360 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 23.80/24.00, Free processors: 3/4.
Currently running:
* qsiprep_wf.single_subject_2001_wf.dwi_preproc_ses_baseline_wf.hmc_sdc_wf.back_to_lps
220928-08:59:15,492 nipype.workflow INFO:
[Node] Setting-up "qsiprep_wf.single_subject_2001_wf.dwi_preproc_ses_baseline_wf.confounds_wf.concat" in "/flywheel/v0/work/qsiprep_wf/single_subject_2001_wf/dwi_preproc_ses_baseline_wf/confounds_wf/concat".
220928-08:59:15,505 nipype.workflow INFO:
[Node] Executing "concat" <qsiprep.interfaces.confounds.GatherConfounds>
220928-08:59:15,535 nipype.workflow INFO:
[Node] Finished "concat", elapsed time 0.028486s.
220928-08:59:15,536 nipype.workflow WARNING:
Storing result file without outputs
220928-08:59:15,537 nipype.workflow WARNING:
[Node] Error on "qsiprep_wf.single_subject_2001_wf.dwi_preproc_ses_baseline_wf.confounds_wf.concat" (/flywheel/v0/work/qsiprep_wf/single_subject_2001_wf/dwi_preproc_ses_baseline_wf/confounds_wf/concat)
220928-08:59:15,538 nipype.workflow ERROR:
Node concat failed to run on host runc.
220928-08:59:15,547 nipype.workflow ERROR:
Saving crash info to /flywheel/v0/output/633310d24deeedf8aadfe1aa/qsiprep/sub-2001/log/20220928-042026_82a9f6ee-37b3-4fd4-8fa5-ee15ae3f4f7b/crash-20220928-085915-root-concat-925661be-b07d-48f3-98a6-b33b2c9dd356.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/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/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, 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 concat.
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 53, in _run_interface
combined_out, confounds_list = _gather_confounds(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 178, in _gather_confounds
raise Exception("Gradients don't match. File a bug report!")
Exception: Gradients don't match. File a bug report!
220928-08:59:31,49 nipype.interface INFO:
Re-orienting /flywheel/v0/work/qsiprep_wf/single_subject_2001_wf/dwi_preproc_ses_baseline_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz to LPS
220928-08:59:51,17 nipype.interface INFO:
Reorienting /flywheel/v0/work/qsiprep_wf/single_subject_2001_wf/dwi_preproc_ses_baseline_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_rotated_bvecs to LPS
220928-08:59:51,38 nipype.workflow INFO:
[Node] Finished "back_to_lps", elapsed time 39.543775s.
[16778553ms INFO ] Command return code: 1
[16778555ms ERROR ] [WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata.
Falling back to 'CITATION'
file none does not exist .
file none does not exist .
file none does not exist .
QSIPrep failed: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/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/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, 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 concat.
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 53, in _run_interface
combined_out, confounds_list = _gather_confounds(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 178, in _gather_confounds
raise Exception("Gradients don't match. File a bug report!")
Exception: Gradients don't match. File a bug report!
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/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/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, 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 concat.
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 53, in _run_interface
combined_out, confounds_list = _gather_confounds(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 178, in _gather_confounds
raise Exception("Gradients don't match. File a bug report!")
Exception: Gradients don't match. File a bug report!
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/python3.8/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 187, in run
self._send_procs_to_workers(updatehash=updatehash, graph=graph)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 347, in _send_procs_to_workers
self._clean_queue(
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 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, 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 concat.
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 53, in _run_interface
combined_out, confounds_list = _gather_confounds(
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/confounds.py", line 178, in _gather_confounds
raise Exception("Gradients don't match. File a bug report!")
Exception: Gradients don't match. File a bug report!
[16778556ms CRITICAL ] The following command has failed:
['qsiprep', '/flywheel/v0/work/bids', '/flywheel/v0/output/633310d24deeedf8aadfe1aa', 'participant', '-v', '--output-resolution=1', '--n_cpus=4', '--mem_mb=24576', '--participant_label=2001', '--skip-bids-validation']
[16778556ms ERROR ] Unable to execute command.
Traceback (most recent call last):
File "/flywheel/v0/run.py", line 307, in main
e_code = run(gear_options, app_options)
File "/flywheel/v0/fw_gear_bids_qsiprep/main.py", line 135, in run
exec_command(
File "/usr/local/miniconda/lib/python3.8/site-packages/flywheel_gear_toolkit/interfaces/command_line.py", line 195, in exec_command
raise RuntimeError("The following command has failed: \n{}".format(command))
RuntimeError: The following command has failed:
['qsiprep', '/flywheel/v0/work/bids', '/flywheel/v0/output/633310d24deeedf8aadfe1aa', 'participant', '-v', '--output-resolution=1', '--n_cpus=4', '--mem_mb=24576', '--participant_label=2001', '--skip-bids-validation']
[16778562ms INFO ] Zipping output file bids-qsiprep_ses-baseline_633310d24deeedf8aadfe1aa.zip
[16790446ms INFO ] Creating viewable archives for all html files
[16790446ms INFO ] Found path: /flywheel/v0/output/633310d24deeedf8aadfe1aa/qsiprep
[16790449ms WARNING ] No *.html files at /flywheel/v0/output/633310d24deeedf8aadfe1aa/qsiprep
[16790451ms INFO ] Previous errors:
Error msg: The following command has failed:
['qsiprep', '/flywheel/v0/work/bids', '/flywheel/v0/output/633310d24deeedf8aadfe1aa', 'participant', '-v', '--output-resolution=1', '--n_cpus=4', '--mem_mb=24576', '--participant_label=2001', '--skip-bids-validation']
[16790451ms INFO ] flywheel/bids-qsiprep Gear is done. Returning 1
Gear completed unsuccessfully after running for 4h39m50.983s.
Uploading results...
Found 2 output file(s) for a total size of 288MB.
The following outputs have been saved:
- bids-qsiprep_ses-baseline_633310d24deeedf8aadfe1aa.zip
- bids_tree.html