fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
The ds_report_t2scomp and ds_report_t2star_hist nodes of init_bold_wf fail due to a missing source_file when I process multi-echo data with --level resampling.
I think this is because the step that sets source_file for reportlet datasink nodes is defined after the workflow is returned when level is resampling:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
result = self._interface.run(cwd=outdir, ignore_exception=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 388, in run
self._check_mandatory_inputs()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: DerivativesDataSink requires a value for input 'source_file'. For a list of required inputs, see DerivativesDataSink.help()
What happened?
The
ds_report_t2scomp
andds_report_t2star_hist
nodes ofinit_bold_wf
fail due to a missingsource_file
when I process multi-echo data with--level resampling
.I think this is because the step that sets
source_file
for reportlet datasink nodes is defined after the workflow is returned when level isresampling
:https://github.com/nipreps/fmriprep/blob/c46c8930751895f0048160fe6715f37f4a290c35/fmriprep/workflows/bold/base.py#L699-L703
What command did you use?
What version of fMRIPrep are you running?
23.2.1
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
No response