I have been running fMRIprep successfully on our university clusters with version 20.0.6 but had an issue with one of my participants which seemed to be caused during skull stripping. I have now manually skull stripped this subject with BET and wanted to use --skull-strip-t1w skip. To do this I asked IT to add the updated version of fMRIprep but I now get the below error (note: I haven’t changed my script or added in the --skull-strip-t1w command yet, so I am not sure what is causing this).
Does anybody have any ideas why this might be? Our IT team replied with:
‘I am guessing this means that the expected format of part of the input has changed. Though it is unclear to me as to what this means needs to be different.’
Output and Error:
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/os-scratch 121G 33M 121G 1% /scratch
working directory: /rds/projects/2018/fernandd-sc-phd/sic613_22011803_12.Z180VN
data directory: /rds/projects/2018/fernandd-sc-phd/chbh00030
/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the
index_metadata arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the
warnings.warn("The ability to pass arguments to BIDSLayout that control "
bids-validator does not appear to be installed
201007-12:04:44,852 nipype.workflow IMPORTANT:
Running fMRIPREP version 20.2.0: * BIDS dataset path: /rds/projects/2018/fernandd-sc-phd/chbh00030/BIDS/rawdata. * Participant list: ['12']. * Run identifier: 20201007-120359_720117d9-2785-4f80-b84a-d76fc9ecd28c. * Output spaces: MNI152NLin2009cAsym:res-native. * Pre-run FreeSurfer's SUBJECTS_DIR: /rds/projects/2018/fernandd-sc-phd/chbh00030/BIDS/derivatives2/freesurfer.
A process has executed an operation involving a call to the
“fork()” system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: [[19386,1],0] (PID 24597)
If you are absolutely sure that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
201007-12:04:47,419 nipype.workflow INFO:
No single-band-reference found for sub-12_ses-AnodOff_task-sart_bold.nii.
201007-12:04:48,513 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
Traceback (most recent call last):
File “/rds/bear-apps/2019a/EL7-haswell/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/multiprocessing/process.py”, line 297, in _bootstrap
File “/rds/bear-apps/2019a/EL7-haswell/software/Python/3.7.2-GCCcore-8.2.0/lib/python3.7/multiprocessing/process.py”, line 99, in run
File “/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/fmriprep/cli/workflow.py”, line 84, in build_workflow
retval[“workflow”] = init_fmriprep_wf()
File “/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/fmriprep/workflows/base.py”, line 64, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File “/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/fmriprep/workflows/base.py”, line 304, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file)
File “/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/fmriprep/workflows/bold/base.py”, line 818, in init_func_preproc_wf
File “/rds/bear-apps/2019a/EL7-haswell/software/FMRIprep/20.2.0-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/fmriprep/workflows/bold/confounds.py”, line 476, in init_carpetplot_wf
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/ants/base.py”, line 75, in init
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 695, in init
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 183, in init
self.inputs = self.input_spec(**inputs)
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/base/specs.py”, line 66, in init
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 135, in validate
self.error(objekt, name, str(value))
File “/rds/bear-apps/2019a/EL7-haswell/software/Nipype/1.5.1-foss-2019a-Python-3.7.2/lib/python3.7/site-packages/traits/base_trait_handler.py”, line 75, in error
object, name, self.full_info(object, name, value), value
traits.trait_errors.TraitError: The ‘input_image’ trait of a _FixTraitApplyTransformsInputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘’ <class ‘str’> was specified.