# QhullError Error when plotting alignment (Self defined OPM sensor configuration) **URL:** \ **Category:** Support & Discussions\ **Tags:** meg, visualization, raw\ **Created:** [April 1, 2025, 5:45pm UTC](https://mne.discourse.group/t/qhullerror-error-when-plotting-alignment-self-defined-opm-sensor-configuration/11049 "2025-04-01T17:45:31Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Luessiaw](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/luessiaw/32/3978_2.png) [@Luessiaw](https://mne.discourse.group/u/Luessiaw)\ **Post date:** [April 1, 2025, 5:45pm UTC](https://mne.discourse.group/t/qhullerror-error-when-plotting-alignment-self-defined-opm-sensor-configuration/11049/1 "2025-04-01T17:45:31Z")
- MNE version: 1.8.0 - operating system: Windows 11 I’m trying to simulate raw data with self defined OPM sensor configuration. Following [this post](https://mne.discourse.group/t/custom-opm-sensor-montages/3159) and [this post](https://mne.discourse.group/t/custom-meg-sensor-configurations-for-simulation/5192) I created a `coil_def.dat` file containing 64 sensors like this: ```python # coil_def.dat 1 9999 2 1 1e-02 0.000e+00 "OPM sensor. Amplitude of Bg: 5.000e-05" 1.000 -1.196e-02 -1.096e-02 1.290e-01 0.000e+00 0.000e+00 1.000e+00 1 9999 2 1 1e-02 0.000e+00 "OPM sensor. Amplitude of Bg: 5.000e-05" 1.000 2.446e-03 2.787e-02 1.270e-01 0.000e+00 0.000e+00 1.000e+00 ... ``` The sensor class, id and accuracy are set as `1, 9999, 2` which represent magnetomter, OPM and accurate representation, respectively (according to [mne doc](https://mne.tools/stable/documentation/implementation.html#the-coil-definition-file)). After reading the file and extracting `sensor_number` and `sensor_locs`, I created my `info`, ```python info = mne.create_info(ch_names=sensor_number, sfreq=100, ch_types="mag" ) # info['dev_head_t'] = mne.transforms.Transform('meg', 'head', np.eye(4)) trans = mne.transforms.Transform("head","mri") for i in range(sensor_number): info["chs"][i]["loc"] = sensor_locs[i] # sensor position and oritation info["chs"][i]["coil_type"] = 9999 # It seems this type represent a custom sensor and can be used for OPM. ``` To verify I checked `info['chs']`, it’s a list of length 64 and every item has a structure as below ```python {'loc': array([-0.01195882, -0.01095526, 0.12898438, 1. , 0. , 0. , 0. , 1. , 0. , 0. , 0. , 1. ]), 'unit_mul': 0 (FIFF_UNITM_NONE), 'range': 1.0, 'cal': 1.0, 'kind': 1 (FIFFV_MEG_CH), 'coil_type': 9999, 'unit': 112 (FIFF_UNIT_T), 'coord_frame': 1 (FIFFV_COORD_DEVICE), 'ch_name': '0', 'scanno': 1, 'logno': 1} ``` A sample anatomy from `mne.datasets` was chosen for simplicity. ```python data_path = mne.datasets.opm.data_path() subject = "OPM_sample" subjects_dir = data_path / "subjects" raw_fname = data_path / "MEG" / "OPM" / "OPM_SEF_raw.fif" bem_fname = subjects_dir / subject / "bem" / f"{subject}-5120-5120-5120-bem-sol.fif" src = mne.setup_source_space(subject,add_dist=False,subjects_dir=subjects_dir) bem = mne.read_bem_solution(bem_fname) ``` Then I tried to compute forward model with `coil_def.dat` and plot alignment, ```python with mne.use_coil_def(opm_coil_def_fname): fwd = mne.make_forward_solution(info, trans, src, bem, eeg=False) fwd = mne.convert_forward_solution(fwd, force_fixed=True, surf_ori=True, use_cps=True) fig = mne.viz.plot_alignment( info, trans=trans, subject=subject, subjects_dir=subjects_dir, # dig=True, coord_frame="mri", surfaces=("head", "white"), bem=bem, ) # kwargs = dict(azimuth=0, elevation=90, distance=0.6, focalpoint=(0.0, 0.0, 0.0)) # mne.viz.set_3d_view(figure=fig, **kwargs) ``` And I got a **QhullError** ```python --------------------------------------------------------------------------- QhullError Traceback (most recent call last) File d:\Anaconda\envs\mne250306\lib\site-packages\mne\viz\_3d.py:1738, in _sensor_shape(coil) 1737 try: -> 1738 tris = _reorder_ccw(rrs, ConvexHull(rrs).simplices) 1739 except QhullError: # 2D geometry likely File _qhull.pyx:2425, in scipy.spatial._qhull.ConvexHull. __init__ () File _qhull.pyx:343, in scipy.spatial._qhull._Qhull. __init__ () QhullError: QH6214 qhull input error: not enough points(1) to construct initial simplex (need 4) While executing: | qhull i Qt Options selected for Qhull 2019.1.r 2019/06/21: run-id 1078245579 incidence Qtriangulate _pre-merge _zero-centrum _maxoutside 0 During handling of the above exception, another exception occurred: IndexError Traceback (most recent call last) Cell In[8], line 4 2 fwd = mne.make_forward_solution(info, trans, src, bem, eeg=False) 3 fwd = mne.convert_forward_solution(fwd, force_fixed=True, surf_ori=True, use_cps=True) ----> 4 fig = mne.viz.plot_alignment( 5 info, 6 trans=trans, 7 subject=subject, 8 subjects_dir=subjects_dir, 9 # dig=True, 10 coord_frame="mri", 11 surfaces=("head", "white"), 12 bem=bem, 13 ) 14 # kwargs = dict(azimuth=0, elevation=90, distance=0.6, focalpoint=(0.0, 0.0, 0.0)) 15 # mne.viz.set_3d_view(figure=fig, **kwargs) File :12, in plot_alignment(info, trans, subject, subjects_dir, surfaces, coord_frame, meg, eeg, fwd, dig, ecog, src, mri_fiducials, bem, seeg, fnirs, show_axes, dbs, fig, interaction, sensor_colors, verbose) File d:\Anaconda\envs\mne250306\lib\site-packages\mne\viz\_3d.py:896, in plot_alignment(info, trans, subject, subjects_dir, surfaces, coord_frame, meg, eeg, fwd, dig, ecog, src, mri_fiducials, bem, seeg, fnirs, show_axes, dbs, fig, interaction, sensor_colors, verbose) 893 # plot sensors (NB snapshot_brain_montage relies on the last thing being 894 # plotted being the sensors, so we need to do this after the surfaces) 895 if picks.size > 0: --> 896 _plot_sensors_3d( 897 renderer, 898 info, 899 to_cf_t, 900 picks, 901 meg, 902 eeg, 903 fnirs, 904 warn_meg, 905 head_surf, 906 "m", 907 sensor_alpha=sensor_alpha, 908 sensor_colors=sensor_colors, 909 ) 911 if src is not None: 912 atlas_ids, colors = read_freesurfer_lut() File d:\Anaconda\envs\mne250306\lib\site-packages\mne\viz\_3d.py:1488, in _plot_sensors_3d(renderer, info, to_cf_t, picks, meg, eeg, fnirs, warn_meg, head_surf, units, sensor_alpha, orient_glyphs, scale_by_distance, project_points, surf, check_inside, nearest, sensor_colors) 1485 from matplotlib.colors import to_rgba_array 1487 defaults = DEFAULTS["coreg"] -> 1488 ch_pos, sources, detectors = _ch_pos_in_coord_frame( 1489 pick_info(info, picks), to_cf_t=to_cf_t, warn_meg=warn_meg 1490 ) 1492 actors = defaultdict(lambda: list()) 1493 locs = defaultdict(lambda: list()) File :12, in _ch_pos_in_coord_frame(info, to_cf_t, warn_meg, verbose) File d:\Anaconda\envs\mne250306\lib\site-packages\mne\viz\_3d.py:1066, in _ch_pos_in_coord_frame(info, to_cf_t, warn_meg, verbose) 1062 coil = _create_meg_coils(this_coil, acc="normal", coilset=coilset)[ 1063 0 1064 ] 1065 # store verts as ch_coord -> 1066 ch_coord, triangles = _sensor_shape(coil) 1067 ch_coord = apply_trans(coil_trans, ch_coord) 1068 if len(ch_coord) == 0 and warn_meg: File d:\Anaconda\envs\mne250306\lib\site-packages\mne\viz\_3d.py:1742, in _sensor_shape(coil) 1740 logger.debug("Falling back to planar geometry") 1741 u, _, _ = np.linalg.svd(rrs.T, full_matrices=False) -> 1742 u[:, 2] = 0 1743 rr_rot = rrs @ u 1744 tris = Delaunay(rr_rot[:, :2]).simplices IndexError: index 2 is out of bounds for axis 1 with size 1 ``` I navigated to `_3d.py` but couldn’t settle the problem. I’ll be appreciated if anybody could tell me what caused the bug or how to fix it. I’m not sure whether I defined my `coil_def.dat` correctly (for example the class, id, accuracy, weight, etc.) Thanks for any advices.