Dear team,
I have recently updated dmriprep from 0.4.0 to 0.5.0 version and am having couple of issues which I did not experience when running earlier version.
I am using following command with docker:
fslicense=/home/sneha/freesurfer_license.txt
docker run -ti -v /home/ubuntu/tracktbi:/inputs -v /home/ubuntu/tracktbi/derivatives:/outputs -v ${fslicense}:/opt/freesurfer/license.txt:ro nipreps/dmriprep:0.5.0 /inputs /outputs participant --participant-label 011011 -v --ignore fieldmaps --use-syn-sdc --output-spaces MNI152NLin6Asym MNI152NLin2009cAsym --low-mem --fs-subjects-dir /outputs/freesurfer --fs-no-reconall --notrack
To begin with, when I run dmriprep with version 0.5.0 with ‘–use-syn-sdc’ argument and ‘–output-space’ as only MNI152NLin6Asym, it gives an error:
RuntimeError: Argument ‘–use-sdc-syn’ requires having ‘MNI152NLin2009cAsym’ as one output standard space. Please add the ‘MNI152NLin2009cAsym’ keyword to the ‘–output-spaces’ argument
It continues to run fine after I added ‘MNI152NLin2009cAsym’ to the ‘–output-spaces’ argument.
I did not get this error when I ran it with v0.4.0. Will MNI152NLin2009cAsym need to be always added with ‘–use-sdc-syn’ flag moving forward (from v0.5.0).
However, dMRIPrep preprocessing did not finish successfully. I get an error towards the end
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 723, in _run_command
cmd = self._interface.cmdline
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 739, in cmdline
allargs = [self._cmd_prefix + self.cmd] + self._parse_inputs()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 995, in _parse_inputs
arg = self._format_arg(name, spec, value)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/ants/resampling.py”, line 505, in _format_arg
return self._get_transform_filenames()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/ants/resampling.py”, line 481, in _get_transform_filenames
"ERROR: The invert_transform_flags list must have the same number "
ValueError: ERROR: The invert_transform_flags list must have the same number of entries as the transforms list.210708-04:03:12,3 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 11.42/11.42, Free processors: 2/2.
210708-04:03:13,998 nipype.workflow INFO:
210708-04:03:13,998 nipype.workflow ERROR:
could not run node: dmriprep_wf.single_subject_011011_wf.syn_preprocessing_auto_00003.prior2epi
210708-04:03:13,998 nipype.workflow INFO:
crashfile: /outputs/dmriprep/sub-011011/log/20210707-193411_4d354cf6-4b80-4d0b-b0ae-38750a919751/crash-20210708-040309-root-prior2epi-21792f50-5182-4a1a-a34d-f6b6105412e7.txt
210708-04:03:13,999 nipype.workflow ERROR:
could not run node: dmriprep_wf.single_subject_011011_wf.syn_preprocessing_auto_00001.prior2epi
210708-04:03:13,999 nipype.workflow INFO:
crashfile: /outputs/dmriprep/sub-011011/log/20210707-193411_4d354cf6-4b80-4d0b-b0ae-38750a919751/crash-20210708-040311-root-prior2epi-51f21a15-dc16-46cc-b510-ddb0118d9856.txt
210708-04:03:13,999 nipype.workflow INFO:
210708-04:03:13,999 nipype.workflow CRITICAL:
dMRIPrep failed: Workflow did not execute cleanly. Check log for details
210708-04:03:14,820 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 011011 (6). Check the HTML reports for details.
210708-04:03:14,820 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 011011 (6). Check the HTML reports for details.
May you please advice what would be causing this error?
Thank you,
Sneha