Hello
This issue is related with the spaces in the folder names.
The was fixed yesterday: OpenMEEG bug for head model
Please update Brainstorm and try again.
Francois
Dear Francois,
after a while I tested OpenMEEG 2.4 on a Mac using Matlab 2016b again. It still does not finish the headmodel calculations. It crashes when the OPENMEEG window shows: āReading MEG leadfieldā.
The Matlab error message is as follows:
Subscripted assignment dimension mismatch.
Error in bst_openmeeg (line 450)
Gain(OPTIONS.iMeg, 
= om_load_full(meggain_file);
Error in bst_headmodeler (line 470)
[Gain, errMessage] = bst_openmeeg(OPTIONS);
Error in panel_headmodel>ComputeHeadModel (line 647)
[OPTIONS, errMessage] = bst_headmodeler(OPTIONS);
Error in panel_headmodel (line 27)
eval(macro_method);
Error in panel_protocols>TreeHeadModel (line 1156)
[OutputFiles, errMessage] = panel_headmodel(āComputeHeadModelā, iChanStudies);
Error in panel_protocols (line 44)
eval(macro_method);
Error in tree_callbacks>@(h,ev)panel_protocols(āTreeHeadModelā,bstNodes) (line 2271)
gui_component(āMenuItemā, jPopup, [], āCompute head modelā, IconLoader.ICON_HEADMODEL, [],
@(h,ev)panel_protocols(āTreeHeadModelā, bstNodes));
Best regards
Marcel
hi Marcel,
can you share the content of the folder:
$HOME/.brainstorm/tmp
it should contain the OpenMEEG files necessary for me to understand
what is happening.
thanks
Alex
Helo Alexandre,
I have similar problem and I was unable to find any further responses to this topic. It happens in only one subject, other subjects I processed before or after went without error. I am running openMEEG version 2.4 on Brainstorm with current update (February 2019), Matlab R2016b, Win 7 64-bit.
Creation of head model hangs on "Reading SEEG leadfield".
Here is the content of $HOME/.brainstorm/tmp https://www.dropbox.com/sh/noiez860h3fz0cl/AAA6SMHKY-chCY_9g-FdNX0ga?dl=0
Matlab produces error message:
Subscripted assignment dimension mismatch.
Error in bst_openmeeg (line 492)
Gain(OPTIONS.iSeeg, : ) = om_load_full(seeggain_file);
Error in bst_headmodeler (line 470)
[Gain, errMessage] = bst_openmeeg(OPTIONS);
Error in panel_headmodel>ComputeHeadModel (line 647)
[OPTIONS, errMessage] = bst_headmodeler(OPTIONS);
Error in panel_headmodel (line 27)
eval(macro_method);
Error in panel_protocols>TreeHeadModel (line 1159)
[OutputFiles, errMessage] = panel_headmodel('ComputeHeadModel', iChanStudies);
Error in panel_protocols (line 44)
eval(macro_method);
Error in tree_callbacks>@(h,ev)panel_protocols('TreeHeadModel',bstNodes) (line 2319)
gui_component('MenuItem', jPopup, [], 'Compute head model', IconLoader.ICON_HEADMODEL, [], @(h,ev)panel_protocols('TreeHeadModel', bstNodes));
Thank you for your time,
Adam
It is weird that this only happens with a single subject, which will suggest that is unrelated to the original issue. But I agree that the error message might not help. It seems like it just hangs and never comes back.
I'll try to reproduce.
Hi Adam,
The bug you get is not coming from OpenMEEG, but from Brainstorm. In the files you sent, we can see that the leadfield was correctly computed (openmeeg_gain_seeg.mat), but it looks like its size does not match what Brainstorm expects at line 492 in bst_openmeeg.
The leadfield matrix computed by openmeeg has 114 rows, but I can't check how many were expected based only on the OpenMEEG files you sent.
If you are comfortable with the Matlab environment, you could try understanding where is the error coming from by placing a breakpoint in bst_openmeeg at line 492 (click at the left of the line), then starting the BEM computation. When the debugger stops, you can explore the contents of the variables.
Otherwise, you could try sending me the files and I could do it for you. Right-click on the subject > file > duplicate subject, then delete all files that are not necessary to run this computation. Then right-click on the subject > File > Export subject, upload the .zip file somewhere, and send me the link as a private message.
Francois
Hello,
I am having trouble computing the head model with BEM for one of my subjects.
The Error that I am getting is the following:
I tried to follow the tutorial and compute the BEM surfaces in brainstorm but this did not work.
Could you please help me with that?
Thank you so much,
Georgios
the error is at the bottom. Did you check that the meshes in your model are nested and non-intersecting?
Alex
1 Like
@Georgios You can copy-paste the full error message from the Matlab command window.