[fmriprep] tCompCorr crashes on empty array?

1

Hi there,

I’m very impressed with the robustness and easiness of converting my datasets to BIDS and throwing them into fmriprep. Thanks a bunch!

I’m currently running a Singularity container on Dutch cloud service for scientists (SurfSara/LISA). The workflow worked fine for three openfmri datasets (ds008, ds102 and ds164). However, now I’m trying my own dataset and it fails to get the confounds matrix. Specifically, the TCompCorr-Node fails for al subjects, in the following way:

Node Name: fmriprep_wf.single_subject_01_wf.func_preproc_task_binocularrivalry_run_01_wf.discover_wf.tcompcor
File: crash-20170807-144733-gholland-tcompcor-6b4fcf74-36b7-4911-89c2-4e00d09ca668.pklz
Working Directory: /scratch/wf/fmriprep_wf/single_subject_01_wf/func_preproc_task_binocularrivalry_run_01_wf/discover_wf/tcompcor
Inputs:
components_file: tcompcor.tsv
compress_report: auto
generate_report: True
header_prefix:
high_pass_cutoff: 128.0
ignore_exception: False
mask_files: [’/scratch/wf/fmriprep_wf/single_subject_01_wf/func_preproc_task_binocularrivalry_run_01_wf/discover_wf/CSF_roi/erodd_mask.nii.gz’]
mask_index:
merge_method:
num_components: 6
out_report: report.html
percentile_threshold: 0.05
pre_filter: cosine
realigned_file: /scratch/wf/fmriprep_wf/single_subject_01_wf/func_preproc_task_binocularrivalry_run_01_wf/epi_reg_wf/merge/vol0000_trans_merged.nii.gz
regress_poly_degree: 1
repetition_time: 0.972075
save_pre_filter: True
use_regress_poly:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py”, line 52, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 372, in run
self._run_interface()
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 482, in _run_interface
self._result = self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 613, in _run_command
result = self._interface.run()
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 1083, in run
runtime = self._run_wrapper(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 1031, in _run_wrapper
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/common/report.py”, line 53, in _run_interface
ReportCapableInterface, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/algorithms/confounds.py”, line 420, in _run_interface
mask_images = self._process_masks(mask_images, imgseries.get_data())
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/algorithms/confounds.py”, line 549, in _process_masks
(1. - self.inputs.percentile_threshold)).astype(int))
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/lib/function_base.py”, line 4116, in percentile
interpolation=interpolation)
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/lib/function_base.py”, line 3858, in _ureduce
r = func(a, **kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/lib/function_base.py”, line 4233, in _percentile
x1 = take(ap, indices_below, axis=axis) * weights_below
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/fromnumeric.py”, line 134, in take
return _wrapfunc(a, ‘take’, indices, axis=axis, out=out, mode=mode)
File “/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/fromnumeric.py”, line 57, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.
Interface TCompCorRPT failed to run.

These are the only errors I get.

Does anyone have a clue what is going on here? It seems to not find any voxels that cross the percentile threshold or something…

And is there a way to still get a confounds matrix, without the tcompcorr components?

Cheers,
Gilles

2

This crash could be unrelated to tCompCor. Could you share the HTML report for this participant? It should be in the output directory.

3

Sure.

4

Even though the BOLD-T1w coregistration seems ok the overlaid aCompCor masks seem off (they should outline the ventricles and white matter). I think something went wrong when the transformation was applied. Could you share data of one example participant so we could fix this?

5

Yeah, it looks like tCompCor isn’t finding any components, which the interface doesn’t handle gracefully. A test file would be very useful in figuring out how best to handle that case.

I also agree that the aCompCor masks are too small. To resolve this, in addition to a BOLD file, we would also need the fmriprep/sub-03/anat/*_probtissue.nii.gz files.

6

Thanks for helping out. I sent one subject to Chris by email.

1 Like
7

AFAIK this should be solved in the latest release. Could you try it out?

8

I don’t get the empty array-error anymore, but now the workflow crashes on a MemoryError, even when using only 4 cpus on a 64GB Node.

The --low-mem flag of this version solves that problem, but is not yet in 1.0.rc2

9

@Gilles_de_Hollander I’ve updated the --low-mem branch to include all of the updates in -rc2, so I’d encourage you to re-download https://github.com/effigies/fmriprep/archive/enh/unzip_option.tar.gz and use that until the next release candidate.

1 Like