Fmriprep: echo_times trait error

Elmsch · January 28, 2019, 4:56pm

Hi everyone,

I am trying to run fmriprep on dual-echo data but get the following error in the very beginning:

singularity run /home/xyz/Documents/poldracklab_fmriprep_1.2.4-2018-12-03-bc59eae67231.img /srv/data/Users/xyz/xyz/Nifti /srv/data/Users/xyz/xyz/Prep participant --participant-label 5 --fs-license-file /home/xyz/Documents/license.txt --write-graph --use-aroma --output-space T1w template --t2s-coreg --fs-no-reconall --n_cpus 48
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
42 Files, 3.24GB xyz T1w
2 - Subjects bold
2 - Sessions sbref
fieldmap

If you have any questions please post on https://neurostars.org/tags/bids

/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/site-packages/skimage/init.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/usr/local/miniconda/lib/python3.6/site-packages/pytest.py’ mode=‘r’ encoding=‘utf-8’>
imp.find_module(‘pytest’)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can’t resolve package from spec or package, falling back on name and path
return f(*args, **kwds)
190128-16:20:54,693 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.2.4:
  * BIDS dataset path: /srv/data/Users/xyz/xyz/Nifti.
  * Participant list: ['5'].
  * Run identifier: 20190128-162054_d055fe42-0a13-41df-a558-4cf630b8eb7f.
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/srv/data/Users/xyz/xyz/Nifti/dataset_description.json’ mode=‘r’ encoding=‘UTF-8’>
self.description = json.load(open(target, ‘r’))
/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/config/bids.json’ mode=‘r’ encoding=‘UTF-8’>
domain = json.load(open(domain, ‘r’))
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/srv/data/Users/xyz/xyz/Nifti/sub-5/ses-001/func/sub-5_ses-001_task-degspeech_echo-1_bold.json’ mode=‘r’ encoding=‘utf-8’>
encoding=‘utf-8’))
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/srv/data/Users/xyz/xyz/Nifti/sub-5/ses-001/func/sub-5_ses-001_task-degspeech_echo-2_bold.json’ mode=‘r’ encoding=‘utf-8’>
encoding=‘utf-8’))
190128-16:20:55,139 nipype.workflow IMPORTANT:
Creating bold processing workflow for “/srv/data/Users/xyz/xyz/Nifti/sub-5/ses-001/func/sub-5_ses-001_task-degspeech_echo-2_bold.nii.gz” (0.85 GB / 1500 TRs). Memory resampled/largemem=3.39/16.13 GB.
190128-16:20:55,140 nipype.workflow IMPORTANT:
No single-band-reference found for sub-5_ses-001_task-degspeech_echo-2_bold.nii.gz
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name=’/srv/data/Users/xyz/xyz/Nifti/sub-5/ses-001/fmap/sub-5_ses-001_phasediff.json’ mode=‘r’ encoding=‘utf-8’>
encoding=‘utf-8’))
190128-16:20:56,301 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
/usr/local/miniconda/lib/python3.6/site-packages/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed
warnings.warn(‘cmp not installed’)
/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py:1887: UserWarning: This has not been fully tested. Please report any failures.
warn(‘This has not been fully tested. Please report any failures.’)
190128-16:20:58,407 nipype.workflow IMPORTANT:
SDC: fieldmap estimation of type “phasediff” intended for /srv/data/Users/xyz/xyz/Nifti/sub-5/ses-001/func/sub-5_ses-001_task-degspeech_echo-2_bold.nii.gz found.
190128-16:20:58,411 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
Process Process-2:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 258, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 738, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 216, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err,
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 505, in init_single_subject_wf
num_bold=len(subject_data[‘bold’]))
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py”, line 501, in init_func_preproc_wf
name=‘bold_t2smap_wf’)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/t2s.py”, line 87, in init_bold_t2s_wf
t2smap_node = pe.Node(T2SMap(echo_times=echo_times), name=‘t2smap_node’)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 789, in init
super(CommandLine, self).init(**inputs)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 181, in init
self.inputs = self.input_spec(**inputs)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/specs.py”, line 67, in init
super(BaseTraitedSpec, self).init(**kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/traits/trait_types.py”, line 2338, in validate
self.error( object, name, value )
File “/usr/local/miniconda/lib/python3.6/site-packages/traits/trait_handlers.py”, line 172, in error
value )
traits.trait_errors.TraitError: The ‘echo_times’ trait of a T2SMapInputSpec instance must be a list of at least 3 items which are a float, but a value of [0.033, 0.012] <class ‘list’> was specified.

Does anyone know what is going wrong here?

Thank you very much for your help!
Elmsch

emdupre · January 28, 2019, 4:59pm

Hi @Elmsch !

Dual-echo handling was updated in the most recent version of fMRIPrep. Could you please upgrade to the latest docker image and let us know if the error persists ?

Elizabeth

Elmsch · January 28, 2019, 5:21pm

Hi @emdupre,

Thanks a lot for your help!

I just reran fmriprep using version 1.2.6 but ended up with the same error.

Elmsch

oesteban · January 28, 2019, 9:14pm

Sorry about this, but you’ll need to update to version 1.2.6-1 (the final “-1” contains the patch for this).