Hi,
I'm trying to run the GLM analysis (measured) example in Visual Studio Code and Jupyter Notebook. I tried copying it and running with my own fNIRS data, and it was crashing after the creation of the contrast, using the plot_topo() method. I then tried using the default dataset, the one used in the original notebook, and still crashes in the same position.
The last part of the error is:
File c:\Users\User\Desktop\mne tutorials\mne_venv\Lib\site-packages\mne_nirs\visualisation_plot_GLM_topo.py:344, in _handle_overlaps(info, t, sphere, estimates)
334 info_subset = pick_info(info, picks)
335 (
336 _,
337 pos,
(...)
342 clip_origin,
343 ) = _prepare_topomap_plot(info_subset, t, sphere=sphere)
--> 344 estmrg, ch_names = _merge_ch_data(estimates.copy()[picks], t, ch_names)
345 return estmrg, pos, ch_names, sphere
IndexError: invalid index to scalar variable.
I do think that estimates is supposed to be a numpy array of dimensions [n x m], n and m > 1, since in _plot_glm_contrast_topo estimates are taken as estimates[0], but contrast.data.effect (as the one generated in the tutorial) is a monodimensional array, so estimates[0] just takes the first element (and not an array), resulting in the previous error. Is my interpretation true? How can I solve it?
Thanks
Hi,
I'm trying to run the GLM analysis (measured) example in Visual Studio Code and Jupyter Notebook. I tried copying it and running with my own fNIRS data, and it was crashing after the creation of the contrast, using the plot_topo() method. I then tried using the default dataset, the one used in the original notebook, and still crashes in the same position.
The last part of the error is:
File c:\Users\User\Desktop\mne tutorials\mne_venv\Lib\site-packages\mne_nirs\visualisation_plot_GLM_topo.py:344, in _handle_overlaps(info, t, sphere, estimates)
334 info_subset = pick_info(info, picks)
335 (
336 _,
337 pos,
(...)
342 clip_origin,
343 ) = _prepare_topomap_plot(info_subset, t, sphere=sphere)
--> 344 estmrg, ch_names = _merge_ch_data(estimates.copy()[picks], t, ch_names)
345 return estmrg, pos, ch_names, sphere
IndexError: invalid index to scalar variable.
I do think that estimates is supposed to be a numpy array of dimensions [n x m], n and m > 1, since in _plot_glm_contrast_topo estimates are taken as estimates[0], but contrast.data.effect (as the one generated in the tutorial) is a monodimensional array, so estimates[0] just takes the first element (and not an array), resulting in the previous error. Is my interpretation true? How can I solve it?
Thanks