Hi,
I am running fmriprep-1.5.4 on singularity using the following code.
singularity run --cleanenv /mnt/tools/fMRIprep_sing/fmriprep-1.5.4.simg /mnt/fMRIPrep/Test1/my_data /mnt/fMRIPrep/Test1/outputs3 -w /mnt/fMRIPrep/Test1/outputs3/derivatives/scratch --fs-license-file $PWD/license.txt --write-graph --cifti-output participant --participant-label sub-50050 --output-spaces MNI152NLin6Asym:res-2 anat fsaverage:den-10k
I am getting same error for both resting state runs. Following I am pasting the error for resting state run 2.
Node Name: fmriprep_wf.single_subject_50050_wf.func_preproc_ses_1_task_rest_run_02_wf.carpetplot_wf.select_std
File: /mnt/fMRIPrep/Test1/outputs3/fmriprep/sub-50050/log/20200114-104808_b64605b9-5d93-4a9b-ba24-5be992d91324/crash-20200114-191028-sameera-select_std-d9b509f7-f73c-4c60-8900-1e69362757aa.txt
Working Directory: /mnt/fMRIPrep/Test1/outputs3/derivatives/scratch/fmriprep_wf/single_subject_50050_wf/func_preproc_ses_1_task_rest_run_02_wf/carpetplot_wf/select_std
Inputs:
key: MNI152NLin2009cAsym
keys: [‘MNI152NLin6Asym’, ‘fsaverage’, ‘MNI152NLin2009cAsym’, ‘fsaverage5’]
std2anat_xfm: [’/mnt/fMRIPrep/Test1/outputs3/derivatives/scratch/fmriprep_wf/single_subject_50050_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin6Asym.res2/registration/ants_t1_to_mniInverseComposite.h5’, ‘/mnt/fMRIPrep/Test1/outputs3/derivatives/scratch/fmriprep_wf/single_subject_50050_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym.res2/registration/ants_t1_to_mniInverseComposite.h5’]
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 314, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 479, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 585, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 678, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 384, in run
outputs = self.aggregate_outputs(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 461, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/utility.py”, line 147, in _list_outputs
for k in self._fields}
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/utility.py”, line 147, in
for k in self._fields}
IndexError: list index out of range
Any suggestion how to fix the issue? Thanks in advance!!
Best Regards
Sameera