fMRIprep error: c3d_affine_tool

1

Dear all,

when running fMRIPrep-20.1.0, I suddenly receive the following error:

   Node: fmriprep_wf.single_subject_5_wf.func_preproc_ses_1_task_rest_run_3_wf.bold_hmc_wf.fsl2itk
    Working directory: /Users/neurolab/work/fmriprep_wf/single_subject_5_wf/func_preproc_ses_1_task_rest_run_3_wf/bold_hmc_wf/fsl2itk

    Node inputs:

    in_files = <undefined>
    in_reference = <undefined>
    in_source = <undefined>
    num_threads = 8

    Traceback (most recent call last):
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
        result["result"] = node.run(updatehash=updatehash)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
        result = self._run_interface(execute=True)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
        return self._run_command(execute)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
        result = self._interface.run(cwd=outdir)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/niworkflows/interfaces/itk.py", line 69, in _run_interface
        for i, in_mat in enumerate(self.inputs.in_files)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
        yield fs.pop().result()
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 435, in result
        return self.__get_result()
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
        raise self._exception
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/concurrent/futures/thread.py", line 57, in run
        result = self.fn(*self.args, **self.kwargs)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/niworkflows/interfaces/itk.py", line 204, in _mat2itk
        resource_monitor=False,
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 781, in _run_interface
        % (executable_name, runtime.hostname)
    OSError: No command "c3d_affine_tool" found on host NeuroLabs-MacBook-Pro.local. Please check that the corresponding package is installed.
        indent preformatted text by 4 spaces
2

Ok. I updated to version 20.2.3 and the following error shows up:

Process Process-2:
Traceback (most recent call last):
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/fmriprep/cli/workflow.py", line 82, in build_workflow
retval["workflow"] = init_fmriprep_wf()
  File "/Users/neurolab/opt/anaconda3/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 "/Users/neurolab/opt/anaconda3/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 "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/fmriprep/workflows/bold/base.py", line 827, in init_func_preproc_wf
name='carpetplot_wf')
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/fmriprep/workflows/bold/confounds.py", line 476, in init_carpetplot_wf
interpolation='MultiLabel'),
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/ants/base.py", line 73, in __init__
super(ANTSCommand, self).__init__(**inputs)
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 703, in __init__
super(CommandLine, self).__init__(**inputs)
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 191, in __init__
self.inputs.trait_set(**inputs)
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/traits/has_traits.py", line 1358, in trait_set
setattr(self, name, value)
  File "/Users/neurolab/opt/anaconda3/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 "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
  File "/Users/neurolab/opt/anaconda3/lib/python3.7/site-packages/traits/base_trait_handler.py", line 77, 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.

I use the following command in python (it worked fine with 20.1.0):

subprocess.run(['fmriprep', str(subject_path), str(subject_path)+'/derivatives/participant/', 'participant', '--fs-subjects-dir', str(path_freesurfer), '--fs-license-file', str(path_fs_license)])

3

At what point does this error show up? Is the dataset BIDS validated?

4

At the beginning. Yes, right I did not specify a task Name in the json files. I changed it and now it is BIDS Validated, but the same error shows up.

It look likes it is handled here:

My Bold file contains 248 timepoints. I am not sure how the issue 1931 could help me

5

I think I made a mistake.

What is actually the difference in the two?:
nipreps/fmriprep
poldracklab/fmriprep

6

You should use nipreps/fmriprep, the most recent version pushed by poldracklab is 20.2.0, which is ~10 months old.

7

Okay, thanks!
Best Steph