Hurray! When removing the ‘–rm’ flag and setting a working directory on another disk, it worked (for most cases)! I still get a couple of errors (below, not sure if these affect follow-up classifier problem), but the output files exist and the group level analysis went off without a hitch!
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 68, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 644, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/interfaces/anatomical.py", line 104, in _run_interface
stats = summary_stats(inudata, pvmdata, airdata, erode=erode)
File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/qc/anatomical.py", line 607, in summary_stats
'p95': float(np.percentile(img[mask == 1], 95)),
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.
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 68, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 480, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 644, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 521, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/mriqc/interfaces/anatomical.py”, line 111, in _run_interface
snrvals.append(snr(stats[tlabel][‘median’], stats[tlabel][‘stdv’], stats[tlabel][‘n’]))
File “/usr/local/miniconda/lib/python3.6/site-packages/mriqc/qc/anatomical.py”, line 228, in snr
return float(mu_fg / (sigma_fg * sqrt(n / (n - 1))))
ZeroDivisionError: float division by zero
Now I am trying to run the random forest classifier, and I get the following error:
IndexError: boolean index did not match indexed array along dimension 0; dimension is 73 but corresponding boolean dimension is 71
The docker version of mriqc that I used is 0.11.0, and the current pip-installable version is 0.12.0… Both 0.12.0 and 0.11.0 gave me the above error. Is it plausible that the group level analysis failed to populate a column of the T1w.csv
table because of one of the above errors?