Hi there,
I’ve been trying to run fMRIPrep on my multi-echo data set but it is failing halfway through everytime. The error I am getting is:
Node: fmriprep_wf.single_subject_01_wf.func_preproc_task_replay_run_01_echo_1_wf.bold_t2smap_wf.t2smap_node
Working directory: /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/bold_t2smap_wf/t2smap_node
Node inputs:
args = <undefined>
echo_times = [0.0132, 0.03011, 0.04702]
environ = {}
fittype = curvefit
in_files = <undefined>
mask_file = <undefined>
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
t2smap -d /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_0/merge/vol0000_unwarped_merged.nii.gz /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_1/merge/vol0000_unwarped_merged.nii.gz /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_2/merge/vol0000_unwarped_merged.nii.gz -e 13.2 30.110000000000003 47.019999999999996 --mask /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/brainextraction_wf/_echoidx_0/masker/clipped_mask.nii.gz --fittype curvefit
Standard output:
Standard error:
INFO t2smap:t2smap_workflow:229 Using output directory: /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/bold_t2smap_wf/t2smap_node
INFO t2smap:t2smap_workflow:239 Loading input data: ['/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_0/merge/vol0000_unwarped_merged.nii.gz', '/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_1/merge/vol0000_unwarped_merged.nii.gz', '/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_replay_run_01_echo_1_wf/unwarp_wf/_echoidx_2/merge/vol0000_unwarped_merged.nii.gz']
INFO t2smap:t2smap_workflow:255 Using user-defined mask
INFO t2smap:t2smap_workflow:258 Computing adaptive T2* map
Killed
Return code: 137
I have just updated fMRIPrep to version 21.0.0 and am using the multi-echo feature for separate echoes; this is the only change I’ve made.
The fMRIPrep parameters I am using are the following:
fmriprep-docker
participant --participant-label
–me-output-echos
–fs-license-file C:\Users\edavid46\Desktop\Pacman\Freesurfer\license.txt
–skull-strip-t1w force
-w
–fs-no-reconall
–skip_bids_validation
Does anyone have any ideas what is going wrong? Thanks in advance!