tcompcor: IndexError: cannot do a non-empty take from an empty axes.

[sentry-io]

Sentry Issue: FMRIPREP-EJ

tcompcor: IndexError: cannot do a non-empty take from an empty axes.

IndexError: cannot do a non-empty take from an empty axes.

[ins0mniac2]

Any resolution to this ? I am having a similar error. Here is the log:

Node: fmriprep_wf.single_subject_921943205_wf.func_preproc_ses_07_task_restingstate_run_01_wf.bold_confounds_wf.tcompcor
Working directory: /tmp/work/fmriprep_wf/single_subject_921943205_wf/func_preproc_ses_07_task_restingstate_run_01_wf/bold_confounds_wf/tcompcor

Node inputs:

components_file = tcompcor.tsv
failure_mode = error
header_prefix = t_comp_cor_
high_pass_cutoff = 128.0
ignore_initial_volumes = 1
mask_files = ['/tmp/work/fmriprep_wf/single_subject_921943205_wf/func_preproc_ses_07_task_restingstate_run_01_wf/bold_confounds_wf/tcc_tfm/highres001_BrainExtractionMask_eroded_trans_boldmsk.nii.gz']
mask_index = <undefined>
merge_method = <undefined>
num_components = 6
percentile_threshold = 0.05
pre_filter = cosine
realigned_file = /tmp/work/fmriprep_wf/single_subject_921943205_wf/func_preproc_ses_07_task_restingstate_run_01_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz
regress_poly_degree = 1
repetition_time = 3.0
save_pre_filter = True
use_regress_poly = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/patches.py", line 51, in _run_interface
    runtime = super(RobustTCompCor, self)._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py", line 531, in _run_interface
    mask_images = self._process_masks(mask_images, imgseries.get_data())
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py", line 701, in _process_masks
    (1. - self.inputs.percentile_threshold)).astype(int))
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3540, in percentile
    a, q, axis, out, overwrite_input, interpolation, keepdims)
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3652, in _quantile_unchecked
    interpolation=interpolation)
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3250, in _ureduce
    r = func(a, **kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3767, in _quantile_ureduce_func
    x1 = take(ap, indices_below, axis=axis) * weights_below
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 181, in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 51, in _wrapfunc
    return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

[oesteban]

@rciric is about to finish a PR that may fix this issue. Could you share some data for us to check?

Related #1586 and nipy/nipype#2878