Hello,
I am able to run the prepare_emptyroom, but when I try the maxfilter command on the prepared data, I get this error. I tried a set of 7 subject data files and 7 empty room files, and each created the error.
- MNE version: 1.7.0
- operating system: Ubuntu 22.04.4 LTS
Here is some of the data I’m working with:
empty_ready is the empty room raw file that went through
In [9]: empty_ready = mne.preprocessing.maxwell_filter_prepare_emptyroom(empty_raw, raw =raw, bads ='union' , verbose=True)
In [10]: empty_ready.info
Out[10]:
<Info | 22 non-empty values
acq_pars: ACQch001 110113 ACQch002 110112 ACQch003 110111 ACQch004 110122 ...
acq_stim: 1 10.000000 1000.000000
bads: 2 items (MEG0443, MEG1622)
ch_names: MEG0113, MEG0112, MEG0111, MEG0122, MEG0123, MEG0121, MEG0132, ...
chs: 204 Gradiometers, 102 Magnetometers, 4 Stimulus
custom_ref_applied: False
description: Vectorview system
dev_head_t: MEG device -> head transform
dig: 135 items (3 Cardinal, 4 HPI, 128 Extra)
events: 1 item (list)
experimenter: MEG (meg)
highpass: 0.1 Hz
hpi_subsystem: 3 items (dict)
line_freq: 60.0
lowpass: 330.0 Hz
meas_date: 2024-01-10 19:25:58 UTC
meas_id: 4 items (dict)
nchan: 310
proj_id: 1 item (ndarray)
proj_name: test
projs: mag_ssp_upright.fif : PCA-v1: off, mag_ssp_upright.fif : PCA-v2: ...
sfreq: 1000.0 Hz
subject_info: 6 items (dict)
>
In [11]: empty_proc = maxwell_filter(empty_ready,origin = (0,0,40), int_order=8, ext_order=3, calibration=cal_data, cross_talk= ct_data, st_duration =6, st_correlation=0.
...: 95 , coord_frame = 'head', head_pos=head_pos)
...:
Maxwell filtering raw data
102 of 102 magnetometer types replaced with T3.
Bad MEG channels being reconstructed: ['MEG0443', 'MEG1622']
Processing 204 gradiometers and 102 magnetometers
Using fine calibration sss_cal_3046_2009-04-29.dat
Adjusting non-orthogonal EX and EY
Adjusted coil positions by (μ ± σ): 0.5° ± 0.4° (max: 2.4°)
Using origin 0.0, 0.0, 40000.0 mm in the head frame
Processing data using tSSS with st_duration=6.0
/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.7/lib/python3.12/site-packages/mne/preprocessing/maxwell.py:2349: RuntimeWarning: invalid value encountered in scalar divide
f"bits/sample ({100 * I_tots[lim_idx] / max_info:0.1f}% of peak "
Using 95/95 harmonic components for 0.000 (80/80 in, 15/15 out)
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[9], line 1
----> 1 empty_proc = maxwell_filter(empty_ready,origin = (0,0,40), int_order=8, ext_order=3, calibration=cal_data, cross_talk= ct_data, st_duration =6, st_correlation=0.95 , coord_frame = 'head', head_pos=head_pos)
File <decorator-gen-358>:12, in maxwell_filter(raw, origin, int_order, ext_order, calibration, cross_talk, st_duration, st_correlation, coord_frame, destination, regularize, ignore_ref, bad_condition, head_pos, st_fixed, st_only, mag_scale, skip_by_annotation, extended_proj, verbose)
File /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.7/lib/python3.12/site-packages/mne/preprocessing/maxwell.py:406, in maxwell_filter(raw, origin, int_order, ext_order, calibration, cross_talk, st_duration, st_correlation, coord_frame, destination, regularize, ignore_ref, bad_condition, head_pos, st_fixed, st_only, mag_scale, skip_by_annotation, extended_proj, verbose)
384 logger.info("Maxwell filtering raw data")
385 params = _prep_maxwell_filter(
386 raw=raw,
387 origin=origin,
(...)
404 extended_proj=extended_proj,
405 )
--> 406 raw_sss = _run_maxwell_filter(raw, **params)
407 # Update info
408 _update_sss_info(raw_sss, **params["update_kwargs"])
File /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.7/lib/python3.12/site-packages/mne/preprocessing/maxwell.py:688, in _run_maxwell_filter(raw, skip_by_annotation, st_duration, st_correlation, st_only, st_when, ctc, coil_scale, this_pos_quat, meg_picks, good_mask, grad_picks, head_pos, info, _get_this_decomp_trans, S_recon, update_kwargs, ignore_ref, reconstruct, copy)
660 def _run_maxwell_filter(
661 raw,
662 skip_by_annotation,
(...)
686 # The time it takes to recompute S and pS themselves is roughly on par
687 # with the np.dot with the data, so not a huge gain to be made there.
--> 688 S_decomp, S_decomp_full, pS_decomp, reg_moments, n_use_in = _get_this_decomp_trans(
689 info["dev_head_t"], t=0.0
690 )
691 update_kwargs.update(reg_moments=reg_moments.copy())
692 if ctc is not None:
File /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne1.7/lib/python3.12/site-packages/mne/preprocessing/maxwell.py:1259, in _get_decomp(trans, all_coils, cal, regularize, exp, ignore_ref, coil_scale, grad_picks, mag_picks, good_mask, mag_or_fine, bad_condition, t, mag_scale, mult)
1257 msg = "Matrix is badly conditioned: %0.0f >= 1000" % cond
1258 if bad_condition == "error":
-> 1259 raise RuntimeError(msg)
1260 elif bad_condition == "warning":
1261 warn(msg)
RuntimeError: Matrix is badly conditioned: 18132836229591732 >= 1000
I found the previous thread about this error, which seemed to indicate issues with head position measurement.
I checked the head position from the participant data:
Is there anything else I can check to troubleshoot this? Any other info I can provide? Does this head position include too large a change?
Thanks for your help,
Megan
