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Error in "Spatiotemporal permutation F-test on full sensor data" tutorial #12927
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Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴 |
Can you paste the full traceback and also the output of |
Hi @larsoner, Thank you for the swift response. Here is the full traceback: stat_fun(H1): min=6.752417666025855e-07 max=38.40836555950498
Running initial clustering …
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
ValueError: Buffer dtype mismatch, expected 'ITYPE_t' but got 'long'
Exception ignored in: 'scipy.sparse.csgraph._traversal._connected_components_undirected'
Traceback (most recent call last):
File "/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py", line 304, in _get_components
_, components = connected_components(adjacency)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Buffer dtype mismatch, expected 'ITYPE_t' but got 'long'
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
File /Users/joebathelt/Downloads/Spatiotemporal F-test full sensor (1).py:15
[12](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:12) tfr_threshold = 15.0
[14](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:14) # run cluster based permutation analysis
---> [15](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:15) cluster_stats = spatio_temporal_cluster_test(
[16](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:16) X,
[17](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:17) n_permutations=1000,
[18](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:18) threshold=tfr_threshold,
[19](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:19) tail=1,
[20](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:20) n_jobs=None,
[21](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:21) buffer_size=None,
[22](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:22) adjacency=tfr_adjacency,
[23](https://file+.vscode-resource.vscode-cdn.net/Users/joebathelt/Downloads/Spatiotemporal%20F-test%20full%20sensor%20(1).py:23) )
File <decorator-gen-306>:12, in spatio_temporal_cluster_test(X, threshold, n_permutations, tail, stat_fun, adjacency, n_jobs, seed, max_step, spatial_exclude, step_down_p, t_power, out_type, check_disjoint, buffer_size, verbose)
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1548, in spatio_temporal_cluster_test(X, threshold, n_permutations, tail, stat_fun, adjacency, n_jobs, seed, max_step, spatial_exclude, step_down_p, t_power, out_type, check_disjoint, buffer_size, verbose)
[1546](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1546) else:
[1547](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1547) exclude = None
-> [1548](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1548) return permutation_cluster_test(
[1549](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1549) X,
[1550](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1550) threshold=threshold,
[1551](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1551) stat_fun=stat_fun,
[1552](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1552) tail=tail,
[1553](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1553) n_permutations=n_permutations,
[1554](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1554) adjacency=adjacency,
[1555](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1555) n_jobs=n_jobs,
[1556](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1556) seed=seed,
[1557](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1557) max_step=max_step,
[1558](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1558) exclude=exclude,
[1559](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1559) step_down_p=step_down_p,
[1560](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1560) t_power=t_power,
[1561](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1561) out_type=out_type,
[1562](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1562) check_disjoint=check_disjoint,
[1563](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1563) buffer_size=buffer_size,
[1564](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1564) )
File <decorator-gen-303>:12, in permutation_cluster_test(X, threshold, n_permutations, tail, stat_fun, adjacency, n_jobs, seed, max_step, exclude, step_down_p, t_power, out_type, check_disjoint, buffer_size, verbose)
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1242, in permutation_cluster_test(X, threshold, n_permutations, tail, stat_fun, adjacency, n_jobs, seed, max_step, exclude, step_down_p, t_power, out_type, check_disjoint, buffer_size, verbose)
[1182](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1182) """Cluster-level statistical permutation test.
[1183](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1183)
[1184](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1184) For a list of :class:`NumPy arrays <numpy.ndarray>` of data,
(...)
[1239](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1239) .. footbibliography::
[1240](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1240) """
[1241](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1241) stat_fun, threshold = _check_fun(X, stat_fun, threshold, tail, "between")
-> [1242](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1242) return _permutation_cluster_test(
[1243](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1243) X=X,
[1244](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1244) threshold=threshold,
[1245](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1245) n_permutations=n_permutations,
[1246](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1246) tail=tail,
[1247](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1247) stat_fun=stat_fun,
[1248](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1248) adjacency=adjacency,
[1249](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1249) n_jobs=n_jobs,
[1250](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1250) seed=seed,
[1251](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1251) max_step=max_step,
[1252](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1252) exclude=exclude,
[1253](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1253) step_down_p=step_down_p,
[1254](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1254) t_power=t_power,
[1255](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1255) out_type=out_type,
[1256](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1256) check_disjoint=check_disjoint,
[1257](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1257) buffer_size=buffer_size,
[1258](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1258) )
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:987, in _permutation_cluster_test(X, threshold, n_permutations, tail, stat_fun, adjacency, n_jobs, seed, max_step, exclude, step_down_p, t_power, out_type, check_disjoint, buffer_size)
[985](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:985) partitions = None
[986](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:986) logger.info("Running initial clustering …")
--> [987](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:987) out = _find_clusters(
[988](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:988) t_obs,
[989](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:989) threshold,
[990](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:990) tail,
[991](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:991) adjacency,
[992](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:992) max_step=max_step,
[993](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:993) include=include,
[994](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:994) partitions=partitions,
[995](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:995) t_power=t_power,
[996](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:996) show_info=True,
[997](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:997) )
[998](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:998) clusters, cluster_stats = out
[1000](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:1000) # The stat should have the same shape as the samples
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:455, in _find_clusters(x, threshold, tail, adjacency, max_step, include, partitions, t_power, show_info)
[453](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:453) for x_in in x_ins:
[454](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:454) if np.any(x_in):
--> [455](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:455) out = _find_clusters_1dir_parts(
[456](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:456) x, x_in, adjacency, max_step, partitions, t_power, ndimage
[457](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:457) )
[458](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:458) clusters += out[0]
[459](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:459) sums.append(out[1])
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:493, in _find_clusters_1dir_parts(x, x_in, adjacency, max_step, partitions, t_power, ndimage)
[491](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:491) """Deal with partitions, and pass the work to _find_clusters_1dir."""
[492](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:492) if partitions is None:
--> [493](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:493) clusters, sums = _find_clusters_1dir(
[494](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:494) x, x_in, adjacency, max_step, t_power, ndimage
[495](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:495) )
[496](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:496) else:
[497](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:497) # cluster each partition separately
[498](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:498) clusters = list()
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:547, in _find_clusters_1dir(x, x_in, adjacency, max_step, t_power, ndimage)
[545](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:545) adjacency = sparse.coo_array(adjacency)
[546](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:546) if sparse.issparse(adjacency) or adjacency is False:
--> [547](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:547) clusters = _get_components(x_in, adjacency)
[548](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:548) elif isinstance(adjacency, list): # use temporal adjacency
[549](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:549) clusters = _get_clusters_st(x_in, adjacency, max_step)
File /opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:311, in _get_components(x_in, adjacency, return_list)
[309](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:309) mask = np.zeros(len(comp_list), dtype=bool)
[310](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:310) for ii, comp in enumerate(components):
--> [311](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:311) comp_list[comp].append(ii)
[312](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:312) mask[comp] += x_in[ii]
[313](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/lib/python3.11/site-packages/mne/stats/cluster_level.py:313) clusters = [np.array(k) for k, m in zip(comp_list, mask) if m]
IndexError: list index out of range ... and here is the output from mne.sys_info(): Platform macOS-15.0.1-arm64-arm-64bit
Python 3.11.3 | packaged by conda-forge | (main, Apr 6 2023, 08:58:31) [Clang 14.0.6 ]
Executable [/opt/homebrew/anaconda3/envs/LonelyEEG/bin/python](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/anaconda3/envs/LonelyEEG/bin/python)
CPU arm (10 cores)
Memory 16.0 GB
Core
├☑ mne 1.8.0 (latest release)
├☑ numpy 1.24.3 (OpenBLAS 0.3.21 with 10 threads)
├☑ scipy 1.11.1
└☑ matplotlib 3.7.2 (backend=module://matplotlib_inline.backend_inline)
Numerical (optional)
├☑ sklearn 1.3.0
├☑ numba 0.57.1
├☑ nibabel 5.0.1
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
├☑ openmeeg 2.5.6
├☑ pandas 2.0.3
├☑ h5io 0.1.7
├☑ h5py 3.8.0
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.39.1 (OpenGL 4.1 Metal - 89.3 via Apple M2 Pro)
├☑ pyvistaqt 0.0.0
├☑ vtk 9.2.6
├☑ qtpy 2.2.0 (PyQt5=5.15.6)
├☑ pyqtgraph 0.13.1
├☑ mne-qt-browser 0.5.0
├☑ ipywidgets 7.7.5
├☑ trame_client 3.4.0
├☑ trame_server 2.17.3
├☑ trame_vtk 2.8.11
├☑ trame_vuetify 2.7.1
└☐ unavailable ipympl
Ecosystem (optional)
├☑ eeglabio 0.0.2-3
├☑ edfio 0.4.4
├☑ mffpy 0.8.0
├☑ pybv 0.7.5
└☐ unavailable mne-bids, mne-nirs, mne-features, mne-connectivity, mne-icalabel, mne-bids-pipeline, neo |
Proposed documentation enhancement
First, thank you for developing MNE-Python and for all the work that went into creating such comprehensive and useful tutorials.
I recently completed the spatiotemporal clustering tutorial for full sensor data using MNE version 1.8. However, when I reached the clustering step, I encountered an error at Line 312 that prevented the clustering from completing successfully:
It seems the issue is related to the format or type of the adjacency matrix, but I’m unsure how to resolve it. Could you please advise on what might be causing this error and any steps I could take to fix it?
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