Hi,
I received an error when running the Maxwell filter step in the MNE-BIDS-Pipeline, saying that the rank of the data in the reference rune does not match the empty room data rank, see below:
[10:55:33] β β preprocessing/_02_maxfilter sub-09 run-01 A critical error occurred. The error message was: Reference run data rank 73.0 does not match empty-room data rank 71.0 after Maxwell filtering. This indicates that the data were processed differently.
Aborting pipeline run. The full traceback is:
Traceback (most recent call last):
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 54, in wrapper
out = memory.cache(func)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 263, in wrapper
out_files = memorized_func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/joblib/memory.py", line 594, in __call__
return self._cached_call(args, kwargs)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/joblib/memory.py", line 537, in _cached_call
out, metadata = self.call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/joblib/memory.py", line 779, in call
output = self.func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4_fix/lib/python3.11/site-packages/mne_bids_pipeline/steps/preprocessing/_02_maxfilter.py", line 264, in run_maxwell_filter
raise RuntimeError(msg)
RuntimeError: Reference run data rank 73.0 does not match empty-room data rank 71.0 after Maxwell filtering. This indicates that the data were processed differently.
This occurred only with a specific subject in the dataset and it has to do with which run I set as reference. If I set mf_reference_run = '03'
, I get the error, however, if I set mf_reference_run = '01'
, then the Maxwell filter step runs fine without an error.
Iβm not sure why the data rank in run 3 would be different than in run 1? Iβm wondering if this has to do with the recently fixed bug about setting the mf_reference_run
parameter to anything else than '01'
?
Could anyone please help?
Many thanks,
MΓ‘tΓ©
System info:
Platform Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.17
Python 3.11.0 | packaged by conda-forge | (main, Jan 14 2023, 12:28:47) [GCC 11.3.0]
Executable /home/ma09/.conda/envs/my_mne1.4_fix/bin/python
CPU x86_64 (32 cores)
Memory 251.4 GB
Core
ββ mne 1.4.2
ββ numpy 1.24.3 (OpenBLAS 0.3.23 with 32 threads)
ββ scipy 1.10.1
ββ matplotlib 3.7.1 (backend=agg)
ββ pooch 1.7.0
ββ jinja2 3.1.2
Numerical (optional)
ββ sklearn 1.2.2
ββ numba 0.57.0
ββ nibabel 5.1.0
ββ nilearn 0.10.1
ββ dipy 1.7.0
ββ openmeeg 2.5.6
ββ pandas 2.0.2
ββ unavailable cupy
Visualization (optional)
ββ pyvista 0.39.1 (OpenGL unavailable)
ββ pyvistaqt 0.0.0
ββ ipyvtklink 0.2.2
ββ vtk 9.2.5
ββ qtpy 2.3.1 (None=None)
ββ pyqtgraph 0.13.3
ββ mne-qt-browser 0.5.1
ββ unavailable ipympl
Ecosystem (optional)
ββ mne-bids 0.13.dev0
ββ mne-bids-pipeline 1.4.0.dev3+gb0cf4a0
ββ unavailable mne-nirs, mne-features, mne-connectivity, mne-icalabel