Hi everyone,
I am unable to use the new "anatomically accurate" view when displaying as graph connectivity results. I can see the option in the Brainstorm interface for about half a second before it disappears. I just updated Brainstorm but the issue remains.
Thanks
Thomas
Hi Thomas,
This display option is only available when you're displaying your connectivity file using the "Display fibers" option (such that you have both the graph and the fibers displayed), not when you're only displaying the graph.
If you do not have the "Display fibers" option, it means you do not have a fibers file added to your subject. Refer to this tutorial page for how to import it: https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity We have a template available if you do not have your own fibers.
Cheers,
Martin
To avoid confusion, I made it so the "anatomically accurate" option does not display even for half a second when opening the connectivity graph: https://github.com/brainstorm-tools/brainstorm3/compare/e0ee2676238d...272ec1ce0e10
Ok thanks!
I works when I load the template fiber tracts to the default anatomy.
I am following up on this topic because I ran into a new issue when using the "display fibers" option. I would like to visualize my PLV results but I get the following error when trying do display the results for some frequency bands. It works with delta and gamma but crashes when I try to do the same for theta/alpha. Do you know what could be the issue?
Thanks,
Thomas
Index exceeds matrix dimensions.
Error in figure_connect>UpdateColormap (line
2406)
Offset = DataPair(DataMask,3);
Error in figure_connect>SetRegionFunction
(line 2781)
UpdateColormap(hFig);
Error in figure_connect>UpdateFigurePlot (line
1922)
SetRegionFunction(hFig, RegionFunction);
Error in
figure_connect>CurrentFreqChangedCallback
(line 188)
UpdateFigurePlot(hFig);
Error in figure_connect (line 26)
eval(macro_method);
Error in bst_figures>FireCurrentFreqChanged
(line 1006)
figure_connect('CurrentFreqChangedCallback',
sFig.hFigure);
Error in bst_figures (line 60)
eval(macro_method);
Error in panel_freq>SetCurrentFreq (line 193)
bst_figures('FireCurrentFreqChanged');
Error in
panel_freq>CreatePanel/SliderCurFreq_Callback
(line 98)
SetCurrentFreq(iCurrentFreq);
Thank you for the bug report, Thomas.
I fixed an issue when switching frequency bands in the fibers display: https://github.com/brainstorm-tools/brainstorm3/commit/3260ebbc3f3f44f58e3a96fd1a04fe0aae01b3fd
However I did not encounter the same error message as you. Let me know if that fixed it, otherwise please give me some more information on reproducing this exact error.
Thanks!
Martin
I think the update solved the issue when displaying PLV data, but it still crashes when I switch between frequency bands on PLV results (the permutation t-tests between my conditions).
I tried changing the stat threshold and the multiple comparison parameters but the issue remains.
However, I noticed that it only crashes when the time is let on 0ms. I can switch between frequencies if I first move to later in the epoch first. Does that make any sense to you?
T
Sorry Thomas, I still can't reproduce the issue on my end. Is it possible you share with me your problematic connectivity file (hopefully you ran this on a template anatomy, if so which one?) and a screen capture of what the bug looks like on your end?
Thanks!
Martin
It is not an issue anymore for my connectivity files, but it happens when I try to switch frequency in my connectivity results files. It is not restricted to a given file. Attached is one example file.
timefreq_pconnectn_plv_no_190227_1556.mat (253 KB)
I am using the ICBM152 template. Also, I don't have any bug to show. It just stays endlessly on "updating figures" and I have the error message below on Matlab:
Matrix dimensions must agree.
Error in figure_connect>GetPairs (line 2282)
DataMask = DataMask == 1 &
MeasureFiberMask == 1;
Error in figure_connect>UpdateColormap (line
2341)
[DataPair, DataMask] = GetPairs(hFig);
Error in figure_connect>SetRegionFunction
(line 2781)
UpdateColormap(hFig);
Error in figure_connect>UpdateFigurePlot (line
1922)
SetRegionFunction(hFig, RegionFunction);
Error in
figure_connect>CurrentFreqChangedCallback
(line 188)
UpdateFigurePlot(hFig);
Error in figure_connect (line 26)
eval(macro_method);
Error in bst_figures>FireCurrentFreqChanged
(line 1006)
figure_connect('CurrentFreqChangedCallback',
sFig.hFigure);
Error in bst_figures (line 60)
eval(macro_method);
Error in panel_freq>SetCurrentFreq (line 193)
bst_figures('FireCurrentFreqChanged');
Error in
panel_freq>CreatePanel/SliderCurFreq_Callback
(line 98)
SetCurrentFreq(iCurrentFreq);
Fixed here:
Oh that's why! Great, thanks François!!
Thanks Francois!