Request for few improvements

Dear Brainstorm developers,

I would like to suggest a few improvements:

  • Could you please change the standard starting time in epoched data to time point zero? In epoched data the windows usually start at time -100 and the time of interest ist usually time 0. It saves a lot of to directly start at time zero.

  • Could you enable deselecting bad channels in spectra of epoched data (It should already work for segmented data)?

  • It would be very useful to have signal topography plot similar to meg and eeg amplitude plot for sEEG/ECoG with just one contact next to each other ordered by electrode without any 3D information.

Thanks for your support!
Marcel

1 Like

Hi Marcel,

Thank you for these great suggestions!

Could you please change the standard starting time in epoched data to time point zero? In epoched data the windows usually start at time -100 and the time of interest ist usually time 0. It saves a lot of to directly start at time zero.

Done: https://github.com/brainstorm-tools/brainstorm3/commit/e8c223a6d2f115856bc2a7d03a2ed2588e79b407

Could you enable deselecting bad channels in spectra of epoched data (It should already work for segmented data)?

I think this is already working... Can you describe an exact sequence of operation, together with the screen capture of the entire desktop, leading to a configuration where it is not possible to set a bad channel from a PSD view?

It would be very useful to have signal topography plot similar to meg and eeg amplitude plot for sEEG/ECoG with just one contact next to each other ordered by electrode without any 3D information.

Done: https://github.com/brainstorm-tools/brainstorm3/commit/fbf0503e844d257ec3ada74aef71d3a14259e52e
New documentation section: https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#A2D_topography

2 Likes

Dear Francois,

thank you for these changes! You are right, marking bad channels in spectra already works. This is also very helpful.
I very much like the new display of sEEG electrodes without 3D positions. I tried it on an ECoG dataset for which not all contact positions were marked yet and I get the following error. As I believe informations for these 2D plot are completely based on contact names, can you please enable 2D display without marked electrode positions?

Best regards
Marcel

BST> Saving scouts in surface: ECOG_tutorial/tess_cortex_pial_low.mat
BST> Warning: The position of the following sensors is not set: G_B1 G_B2 G_B3 G_B4 G_B5 G_B6 G_B7 G_B8 G_C1 G_C2 G_C3 G_C4 G_C5 G_C6 G_C7 G_C8 G_D1 G_D2 G_D3 G_D4 G_D5 G_D6 G_D7 G_D8 G_E1 G_E2 G_E3 G_E4 G_E5 G_E6 G_E7 G_E8 G_F1 G_F2 G_F3 G_F4 G_F5 G_F6 G_F7 G_F8 G_G1 G_G2 G_G3 G_G4 G_G5 G_G6 G_G7 G_G8 G_H1 G_H2 G_H3 G_H4 G_H5 G_H6 G_H7 G_H8 IHA1 IHA2 IHA3 IHA4 IHB2 IHB3 IHB4 IHC1 IHC2 IHC3 IHC4
Error using ./
Matrix dimensions must agree.

Error in panel_ieeg>AlignContacts (line 2211)
NewLoc = ((sElectrodes(iElec).Loc(:,1) * w1 + sElectrodes(iElec).Loc(:,2) * w2) ./ (w1 + w2))';

Error in panel_ieeg (line 30)
eval(macro_method);

Error in figure_3d>PlotSensors3D (line 2667)
Channel = panel_ieeg('AlignContacts', iDS, iFig, 'default', sElectrodes, Channel);

Error in figure_3d (line 40)
eval(macro_method);

Error in figure_topo>CreateTopo3dElectrodes (line 1303)
[PlotHandles.hSurf, MarkersLocs2D] = figure_3d('PlotSensors3D', iDS, iFig, Channel, ChanLoc, TopoType);

Error in figure_topo>PlotFigure (line 496)
CreateTopo3dElectrodes(iDS, iFig, Channel(selChan), markers_loc(selChan,:), TopoInfo.TopoType);

Error in figure_topo (line 27)
eval(macro_method);

Error in view_topography (line 379)
isOk = figure_topo('PlotFigure', iDS, iFig, 1);

Error in tree_callbacks>@(h,ev)view_topography(FileName,Modality,'2DElectrodes') (line 2658)
gui_component('MenuItem', jMenu, [], '2D Electrodes', IconLoader.ICON_CHANNEL, [], @(h,ev)view_topography(FileName, Modality,
'2DElectrodes'));

Hi Marcel,

I fixed many small bugs in the ECOG/SEEG display.
I could not reproduce this specific error, but maybe it is already fixed.
Could you update Brainstorm and try again?

Thanks
Francois

It works now and looks excellent! Thanks Francois