Hi,
I recently started to use fmriprep to prep-process our fmri data.
I am getting an error when I tried to process multi-echo data. I haven’t seen this error when I process single echo data. Following you can find the fmriprep command I used and the error,
Fmriprep command: fmriprep /gpfs/projects/fmriprep/test /gpfs/projects/fmriprep/test_outputs -w /gpfs/projects/fmriprep/test_outputs/derivatives/scratch --t2s-coreg --write-graph --cifti-output participant --participant-label sub-13023
Error,
Node Name: fmriprep_wf.single_subject_13023_wf.func_preproc_ses_1_task_Insight2_run_01_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate
File: `/gpfs/projects/fmriprep/test_outputs/fmriprep/sub-13023/log/20190908-104336_c8903beb-1cfc-4488-a74d-4b7fabe30bd2/crash-20190908-110915-sabeykoon-pre_mask_dilate.a0-158e7553-4307-47a0-a8bf-0ec3002d6c45.txt`
Working Directory: `/gpfs/projects/fmriprep/test_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/pre_mask_dilate`
Inputs:
* args: ``
* environ: `{'FSLOUTPUTTYPE': 'NIFTI_GZ'}`
* in_file: `/gpfs/projects/fmriprep/test_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz`
* internal_datatype: `char`
* kernel_file: ``
* kernel_shape: `sphere`
* kernel_size: `3.0`
* nan2zeros: ``
* operation: `max`
* out_file: ``
* output_datatype: ``
* output_type: `NIFTI_GZ`
Traceback (most recent call last): File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run result = self._run_interface(execute=True) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface return self._run_command(execute) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command result = self._interface.run(cwd=outdir) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 369, in run runtime = self._run_interface(runtime) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface self.raise_exception(runtime) File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 689, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: fslmaths -dt char /gpfs/projects/fmriprep/test_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/projects/fmriprep/test_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz Standard output: Standard error: terminate called after throwing an instance of 'NiftiException' what(): Error: cant open file /gpfs/projects/fmriprep/test_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz Return code: -6
Does anyone seen this error before? Can you help me to fix this issue.
Thanks in advance