I’m running nibetaseries on a series of runs and participants using fmriprep. All of my subjects have somewhere around 4-6 runs, they are all in BIDS format, and they all include fmripep files necessary for nibetaseries to run. I’m running at the participant level so in this case it gives me output files for every run.
My problem is that nibetaseries properly runs on half of these participants, and then the other half it runs on all of their runs except for 1-2 of them.
The error I get isn’t super helpful because I can’t tell where it’s coming from. It looks like this:
Traceback (most recent call last):
File “/opt/miniconda-latest/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/opt/miniconda-latest/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 473, in run
result = self._run_interface(execute=True)
File “/opt/miniconda-latest/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 557, in _run_interface
File “/opt/miniconda-latest/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 637, in _run_command
result = self._interface.run(cwd=outdir)
File “/opt/miniconda-latest/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 375, in run
runtime = self._run_interface(runtime)
File “/opt/miniconda-latest/lib/python3.7/site-packages/nibetaseries/interfaces/nistats.py”, line 90, in _run_interface
File “/opt/miniconda-latest/lib/python3.7/site-packages/nistats/first_level_model.py”, line 441, in fit
File “/opt/miniconda-latest/lib/python3.7/site-packages/nistats/design_matrix.py”, line 411, in make_first_level_design_matrix
matrix, _ = full_rank(matrix)
File “/opt/miniconda-latest/lib/python3.7/site-packages/nistats/utils.py”, line 256, in full_rank
U, s, V = spl.svd(X, full_matrices=False)
File “/opt/miniconda-latest/lib/python3.7/site-packages/scipy/linalg/decomp_svd.py”, line 109, in svd
a1 = _asarray_validated(a, check_finite=check_finite)
File “/opt/miniconda-latest/lib/python3.7/site-packages/scipy/_lib/_util.py”, line 239, in _asarray_validated
a = toarray(a)
File “/opt/miniconda-latest/lib/python3.7/site-packages/numpy/lib/function_base.py”, line 496, in asarray_chkfinite
“array must not contain infs or NaNs”)
ValueError: array must not contain infs or NaNs
My regressors tsv file has no NaN values so it can’t be coming from that.
Any help appreciated !