Hello!
I am using the same codes to run 4 subjects with fmriprep, and 3 of them were preprocessed successfully, with one subject stopped at the middle.
the error is:
traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 342, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py”, line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 162, in run
self._clean_queue(jobid, graph, result=result))
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 224, in _clean_queue
raise RuntimeError("".join(result[‘traceback’]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 471, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 555, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 522, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/nilearn.py”, line 126, in _run_interface
new_nii = concat_imgs(self.inputs.in_files, dtype=self.inputs.dtype)
File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py”, line 449, in concat_niimgs
niimg = check_niimg(niimg, ensure_ndim=ndim)
File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py”, line 271, in check_niimg
niimg = load_niimg(niimg, dtype=dtype)
File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg.py”, line 116, in load_niimg
dtype = _get_target_dtype(niimg.get_data().dtype, dtype)
File “/usr/local/miniconda/lib/python3.6/site-packages/nibabel/dataobj_images.py”, line 202, in get_data
data = np.asanyarray(self._dataobj)
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/numeric.py”, line 544, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py”, line 356, in array
raw_data = self.get_unscaled()
File “/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py”, line 351, in get_unscaled
mmap=self._mmap)
File “/usr/local/miniconda/lib/python3.6/site-packages/nibabel/volumeutils.py”, line 525, in array_from_file
infile.seek(offset)
File “indexed_gzip/indexed_gzip.pyx”, line 430, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
The codes I used for running:
singularity run -e --bind /projects/kuhl_lab/yzhao17:/projects/kuhl_lab/yzhao17 /projects/kuhl_lab/yzhao17/Image/fmriprep.simg /projects/kuhl_lab/yzhao17/DIIN/bids_data /projects/kuhl_lab/yzhao17/DIIN/derivatives participant --participant_label 01 --output-space T1w template fsaverage6 --medial-surface-nan -w /projects/kuhl_lab/yzhao17/DIIN/bids_data/works --resource-monitor --notrack --stop-on-first-crash
The data passed bids format check, and I don’t think there is any difference between subjects. I am wondering what’s going on.
Does anyone have any idea about this problem?
thank you so much!