🐛 [User-reported Bug] FileNotFoundError for output 'out_file' of a TShift interface

[DongHyoek]

Describe the bug

I have different subjects, but they are in BIDS Folder format with the same number of files and the same description. I also use the same Data Config (BIDS default setting) and pipeline_config(default).

However, I am getting a 'slice-timing error' on one subject ( another is success). After tracking down the cause, I deduced that the subject with the error in the '_scan_rest' folder in the 'working' folder was trying to process using the 'BLIP_AP_bold.nii.gz' file instead of the 'AP_bold.nii.gz' file I am trying to use.

I'm wondering why this is happening when we use the same formatted BIDS folder and configuration file? Also, if I use the default BIDS data_config, is it possible that the file load for each subject is different when I specify functionalTemplate as None?

The error code is below.

Node: cpac_sub-81274002_ses-1.func_slice_timing_correction_143.slice_timing
Working directory: /home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/func_slice_timing_correction_143/_scan_rest/slice_timing

Node inputs:

args =
environ = {}
ignore =
in_file = /home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/func_slice_timing_correction_143/_scan_rest/slice_timing/sub-81274002_task-rest_desc-REST_MB3_BLIP_AP_bold_resample_calc.nii.gz
interp =
num_threads = 1
out_file =
outputtype = NIFTI_GZ
rlt =
rltplus =
slice_encoding_direction = k
slice_timing =
tpattern = @/home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/_scan_rest/bold_scan_params_sub-81274002_ses-1/tpattern.txt
tr = 2.0s
tslice =
tzero =

Traceback (most recent call last):
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
node.run(updatehash=updatehash)
File "/code/CPAC/pipeline/nipype_pipeline_engine/engine.py", line 428, in run
return super().run(updatehash)
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node slice_timing.

Cmdline:
3dTshift -prefix sub-81274002_task-rest_desc-REST_MB3_BLIP_AP_bold_resample_calc_tshift.nii.gz -tpattern @/home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/_scan_rest/bold_scan_params_sub-81274002_ses-1/tpattern.txt -TR 2.0s /home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/func_slice_timing_correction_143/_scan_rest/slice_timing/sub-81274002_task-rest_desc-REST_MB3_BLIP_AP_bold_resample_calc.nii.gz
Stdout:

Stderr:
++ 3dTshift: AFNI version=AFNI_23.3.09 (Dec 8 2023) [64-bit]
[7m** FATAL ERROR:[0m -ignore value 0 is too large
** Program compile date = Dec 8 2023
Traceback:
Traceback (most recent call last):
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of a TShiftOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/func_slice_timing_correction_143/_scan_rest/slice_timing/sub-81274002_task-rest_desc-REST_MB3_BLIP_AP_bold_resample_calc_tshift.nii.gz' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/code/CPAC/pipeline/nipype_pipeline_engine/monkeypatch.py", line 43, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/home/sdh00/ASD_Sev_Research/snu_cpac_error_check/working/pipeline_cpac-default-pipeline/cpac_sub-81274002_ses-1/func_slice_timing_correction_143/_scan_rest/slice_timing/sub-81274002_task-rest_desc-REST_MB3_BLIP_AP_bold_resample_calc_tshift.nii.gz' for output 'out_file' of a TShift interface

To reproduce

No response

Preconfig

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

Custom pipeline configuration

No response

Run command

No response

Expected behavior

Cause func preprocessing error

Acceptance criteria

Check the logic of data_config and input files

Screenshots

No response

C-PAC version

v1.8.6

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response

[sgiavasis]

Hi @DongHyoek,

I can try to help you get running - could you post your data config file?