Hello,
I am using fmriprep. I am using the latest fmriprep-docker app.
The command I executed was:fmriprep-docker ./ ./derivatives --fs-license $FREESURFER_HOME/license.txt --output-spaces MNIInfant:res-2:cohort-1
I get the following error.
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 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/itk.py”, line 52, in _run_interface
for i, in_mat in enumerate(self.inputs.in_files)]
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 586, in result_iterator
yield fs.pop().result()
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 432, in result
return self.__get_result()
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 384, in __get_result
raise self._exception
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/thread.py”, line 57, in run
result = self.fn(*self.args, **self.kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/itk.py”, line 218, in _mat2itk
fsl2ras=True, itk_transform=out_file, resource_monitor=False).run()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 792, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 723, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
c3d_affine_tool -ref /tmp/work/fmriprep_wf/single_subject_CC00120XX05_wf/func_preproc_ses_41600_task_rest_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz -src /tmp/work/fmriprep_wf/single_subject_CC00120XX05_wf/func_preproc_ses_41600_task_rest_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz /tmp/work/fmriprep_wf/single_subject_CC00120XX05_wf/func_preproc_ses_41600_task_rest_wf/bold_hmc_wf/mcflirt/sub-CC00120XX05_ses-41600_task-rest_bold_valid_mcf.nii.gz.mat/MAT_0084 -fsl2ras -oitk /tmp/work/fmriprep_wf/single_subject_CC00120XX05_wf/func_preproc_ses_41600_task_rest_wf/bold_hmc_wf/fsl2itk/tmp-w8j42xpp/MAT_0084_itk-00084.txt
Standard output:
Standard error:
terminate called after throwing an instance of ‘char const*’
Aborted (core dumped)
Return code: 134
Can you help me resolve this?
Thanks!
Swati