Hi, fmriprep is producing 2 types of errors while preprocessing 5 subjects (on 36 subject set). They don’t appear together - it’s either one or another and both are fatal to the pipeline. I can’t clear them and am getting frustrated. I’m pasting them below and would appreciate any info on how to approach it?
The set has one T1 and 5 functional runs (4x MB & 1x MPRAGE).
I’m using fMRIPrep-20.0.7 via Singularity container; no surface reconstruction.
If you need more info let me know.
Error log 1 (coming up in 3 subjects).:
> Node: fmriprep_wf.single_subject_19_wf.func_preproc_task_run01_wf.bold_stc_wf.slice_timing_correction
> Working directory: /home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction
>
> Node inputs:
>
> args = <undefined>
> environ = {}
> ignore = 0
> in_file = /home/xxx/xxx/projects/RSA/niftii/sub-19/func/sub-19_task-run01_bold.nii.gz
> interp = <undefined>
> num_threads = 1
> out_file = <undefined>
> outputtype = NIFTI_GZ
> rlt = <undefined>
> rltplus = <undefined>
> slice_encoding_direction = k
> slice_timing = [0.0, 0.94, 1.8825, 0.815, 1.7575, 0.69, 1.63, 0.565, 1.505, 0.44, 1.38, 0.3125, 1.255, 0.1875, 1.13, 0.0625, 1.005, 1.945, 0.8775, 1.82, 0.7525, 1.695, 0.6275, 1.5675, 0.5025, 1.4425, 0.3775, 1.3175, 0.25, 1.1925, 0.125, 1.0675, 0.0, 0.94, 1.8825, 0.815, 1.7575, 0.69, 1.63, 0.565, 1.505, 0.44, 1.38, 0.3125, 1.255, 0.1875, 1.13, 0.0625, 1.005, 1.945, 0.8775, 1.82, 0.7525, 1.695, 0.6275, 1.5675, 0.5025, 1.4425, 0.3775, 1.3175, 0.25, 1.1925, 0.125, 1.0675]
> tpattern = <undefined>
> tr = 2s
> tslice = <undefined>
> tzero = <undefined>
>
> 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 516, in run
> result = self._run_interface(execute=True)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
> return self._run_command(execute)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
> result = self._interface.run(cwd=outdir)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
> runtime = self._run_interface(runtime)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 125, in _run_interface
> runtime, correct_return_codes
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 792, in _run_interface
> self.raise_exception(runtime)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 723, in raise_exception
> ).format(**runtime.dictcopy())
> RuntimeError: Command:
> 3dTshift -ignore 0 -prefix sub-19_task-run01_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz
> Standard output:
>
> Standard error:
> ++ 3dTshift: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit]
> e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
> such as /home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz,
> or viewing/combining it with volumes of differing obliquity,
> you should consider running:
> 3dWarp -deoblique
> on this and other oblique datasets in the same session.
> See 3dWarp -help for details.
> ++ Oblique dataset:/home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz is 10.579273 degrees from plumb.
> ++ WARNING: nifti_read_buffer(/home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz):
> data bytes needed = 1179648
> data bytes input = 902945
> number missing = 276703 (set to 0)
> ** load bricks: cannot read brick 257 from '/home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz'
> e[7m** ERROR:e[0m EDIT_full_copy: input sub-brick 0 is NULL
> + Dataset /home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz
> e[7m** FATAL ERROR:e[0m Can't copy input dataset '/home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_19_wf/func_preproc_task_run01_wf/bold_stc_wf/slice_timing_correction/sub-19_task-run01_bold.nii.gz'
> ** Program compile date = Jun 12 2017
> Return code: 1
Error Log 2 (2 participants)
> Node: fmriprep_wf.single_subject_16_wf.func_preproc_task_run01_wf.bold_reference_wf.validate
> Working directory: /home/xxx/xxx/projects/RSA/work/fmriprep_wf/single_subject_16_wf/func_preproc_task_run01_wf/bold_reference_wf/validate
>
> Node inputs:
>
> in_file = /home/xxx/xxx/projects/RSA/niftii/sub-16/func/sub-16_task-run01_bold.nii.gz
>
> 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 516, in run
> result = self._run_interface(execute=True)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
> return self._run_command(execute)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
> result = self._interface.run(cwd=outdir)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
> runtime = self._run_interface(runtime)
> File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/images.py", line 474, in _run_interface
> img.to_filename(out_fname)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py", line 334, in to_filename
> self.to_file_map()
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/analyze.py", line 1010, in to_file_map
> data = np.asanyarray(self.dataobj)
> File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/numeric.py", line 553, in asanyarray
> return array(a, dtype, copy=False, order=order, subok=True)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 391, in __array__
> arr = self._get_scaled(dtype=dtype, slicer=())
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 358, in _get_scaled
> scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/arrayproxy.py", line 337, in _get_unscaled
> mmap=self._mmap)
> File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/volumeutils.py", line 534, in array_from_file
> getattr(infile, 'name', 'object')))
> OSError: Expected 719585280 bytes, got 210561894 bytes from object
> - could the file be damaged?