Slice time correction in SLURM HCP failss

1

When running fmriprep on a new HCP cluster with slurm I receive the error that slice time correction does not work:
I allocated 16cpus and 32GB or RAM

220314-12:07:45,577 nipype.workflow WARNING:
Previous output generated by version 0+unknown found.
220314-12:07:45,591 nipype.workflow IMPORTANT:

Running fMRIPREP version 20.2.7:
  * BIDS dataset path: /input.
  * Participant list: ['001'].
  * Run identifier: 20220314-120738_1159855f-b030-4c9b-be16-47774b1c82a5.
  * Output spaces: MNI152NLin2009cAsym:res-native.
  * Pre-run FreeSurfer's SUBJECTS_DIR: /output/freesurfer.

220314-12:07:46,382 nipype.workflow INFO:
No single-band-reference found for sub-001_ses-5_task-rest_run-03_bold.nii.gz.
220314-12:07:46,960 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 1.22e+03s.
220314-12:07:48,872 nipype.workflow INFO:
fMRIPrep workflow graph with 376 nodes built successfully.
220314-12:07:58,993 nipype.workflow IMPORTANT:
fMRIPrep started!
220314-12:08:39,203 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_001_wf.anat_preproc_wf.fs_isrunning” in “/workdir/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/fs_isrunning”.
220314-12:08:39,262 nipype.workflow INFO:
[Node] Executing “fs_isrunning” <nipype.interfaces.utility.wrappers.Function>
220314-12:08:39,321 nipype.workflow INFO:
[Node] Finished “fs_isrunning”, elapsed time 0.000883s.
220314-12:08:40,195 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_001_wf.func_preproc_ses_5_task_rest_run_03_wf.bold_stc_wf.slice_timing_correction” in “/workdir/fmriprep_wf/single_subject_001_wf/func_preproc_ses_5_task_rest_run_03_wf/bold_stc_wf/slice_timing_correction”.
220314-12:08:40,274 nipype.workflow INFO:
[Node] Executing “slice_timing_correction” <nipype.interfaces.afni.preprocess.TShift>
220314-12:08:42,640 nipype.workflow INFO:
[Node] Finished “slice_timing_correction”, elapsed time 2.336845s.
220314-12:08:42,640 nipype.workflow WARNING:
Storing result file without outputs
220314-12:08:42,641 nipype.workflow WARNING:
[Node] Error on “fmriprep_wf.single_subject_001_wf.func_preproc_ses_5_task_rest_run_03_wf.bold_stc_wf.slice_timing_correction” (/workdir/fmriprep_wf/single_subject_001_wf/func_preproc_ses_5_task_rest_run_03_wf/bold_stc_wf/slice_timing_correction)
220314-12:08:43,258 nipype.workflow ERROR:
Node slice_timing_correction failed to run on host srvdgx1.
220314-12:08:43,267 nipype.workflow ERROR:
Saving crash info to /output/fmriprep/sub-001/log/20220314-120738_1159855f-b030-4c9b-be16-47774b1c82a5/crash-20220314-120843-swunderl-slice_timing_correction-1be7c3a3-c2a7-461e-8a34-9cf80f1aee16.txt
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 521, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 639, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 751, in _run_command
f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node slice_timing_correction.

2

Hi,

Is slice timing information present in a BIDS valid JSON file? What was the command you used?

This seems suspiciously high.

Best,
Steven

3

Oh yes, you are absolutely right:
“SliceTiming”: [1255, 0, 1322.5, 70, 1392.5, 137.5, 1462.5, 207.5, 1532.5, 277.5, 1602.5, 347.5, 1672.5, 417.5, 1742.5, 487.5, 1812.5, 557.5, 1882.5, 627.5, 1950, 695, 2020, 765, 2090, 835, 2160, 905, 2230, 975, 2300, 1045, 2370, 1115, 2440, 1185],

could it be that the 1000 point was shifted? or seconds and milliseconds?

4

Slice timing should be in seconds, try changing this and try again.

5

yes now it works. Is there a way to automatically change the dot for 1000 for all .json files?

6

If you know python you can write a script with the json library to manipulate the json files.