DUNEuro error with the tutorial dataset

YRW · February 9, 2022, 9:25am

when I run the "FEM advanced tutorial with MEG/EEG Median nerve stimulation"， I follow all the steps as the tutorial say. When I come to the step "Forward Model\ MEG with DTI tensors" error occur


dipole_9648.time = 0 
dipole_9649.density = sparse 
dipole_9649.time = 0 
dipole_9650.density = sparse 
dipole_9650.time = 0 
Dune reported error: Dune::Exception [findEntityImpl:/home/juan/bst-duneuro/src/duneuro/duneuro/common/edgehopping.hh:84]: coordinate is outside of the grid, or grid is not convex 

status =

    -1


***************************************************************************
** Error: Error during the DUNEuro computation, see logs in the command window.
***************************************************************************

I use the FEM mesh

Name: Subject01/tess_fem_simnibs_718392V.mat
---------------------------------------------------
  |  
  |- Comment:      'FEM 718392V (simnibs, 5 layers)'
  |- Vertices:     [718392x3 double]
  |- Elements:     [3984445x4 double]
  |- Tissue:       [3984445x1 double]
  |- TissueLabels: {1x5 cell}
  |- Tensors:      [3984445x12 double]
  |- History:      {2x3 cell}

can somebody help me, thanks

Francois · February 10, 2022, 1:37pm

Please share your subject, it would be the fastest way for us to reproduce your error and find a solution:

right-click on the subject folder > File > Export subject
upload the .zip file somewhere
post the download link there

Please include a screen capture of the forward model and DUNEuro option windows you are using.

Thanks

@tmedani @juangpc

YRW · February 10, 2022, 2:36pm

Thank you, I have send the .zip file and the DUNEuro option windows to your E-mail

Francois · February 10, 2022, 3:45pm

Please post the here, as it will mostly be useful for @tmedani and/or @juangpc

YRW · February 11, 2022, 9:39am

Download link: 文件分享

tmedani · February 12, 2022, 1:27am

Hi there,

To make sure, you are computing only the MEG right?

Have you generated the mesh using the iso2mesh option, the error may accrue when some hole are present on the mesh, as explained in this step:
https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve?highlight=(fem)#Remesh_with_Iso2mesh

YRW · February 12, 2022, 8:25am

when I use the iso2mesh as tutorial say, the error occur

BST> Plugin iso2mesh already loaded: C:\Users\27848\.brainstorm\plugins\iso2mesh
Fixing asin tolerance to 1.745329e-004 
meshfix C:\Users\27848\.brainstorm\tmp\pre_sclean.off 
Cleaning intersections, degeneracies ... 
Saving output mesh to 'C:\Users\27848\.brainstorm\tmp\pre_sclean_fixed.off' 
Fixing asin tolerance to 1.745329e-004 
meshfix C:\Users\27848\.brainstorm\tmp\pre_sclean.off 
Cleaning intersections, degeneracies ... 
Saving output mesh to 'C:\Users\27848\.brainstorm\tmp\pre_sclean_fixed.off' 
Fixing asin tolerance to 1.745329e-004 
meshfix C:\Users\27848\.brainstorm\tmp\pre_sclean.off 
Cleaning intersections, degeneracies ... 
Saving output mesh to 'C:\Users\27848\.brainstorm\tmp\pre_sclean_fixed.off' 
Fixing asin tolerance to 1.745329e-004 
meshfix C:\Users\27848\.brainstorm\tmp\pre_sclean.off 
Cleaning intersections, degeneracies ... 
Saving output mesh to 'C:\Users\27848\.brainstorm\tmp\pre_sclean_fixed.off' 
Fixing asin tolerance to 1.745329e-004 
meshfix C:\Users\27848\.brainstorm\tmp\pre_sclean.off 
Cleaning intersections, degeneracies ... 
Saving output mesh to 'C:\Users\27848\.brainstorm\tmp\pre_sclean_fixed.off' 
BST> Emptying temporary directory...
BST> Plugin iso2mesh already loaded: C:\Users\27848\.brainstorm\plugins\iso2mesh
 
FEM> 1. scalp: D:\BrainSuite\brainstorm_db\TutorialFem1\anat\Subject01\tess_scalp.mat
FEM> 2. skull: D:\BrainSuite\brainstorm_db\TutorialFem1\anat\Subject01\tess_skull.mat
FEM> 3. white: D:\BrainSuite\brainstorm_db\TutorialFem1\anat\Subject01\tess_white.mat
FEM> 4.  gray: D:\BrainSuite\brainstorm_db\TutorialFem1\anat\Subject01\tess_gray.mat
FEM> 5.   csf: D:\BrainSuite\brainstorm_db\TutorialFem1\anat\Subject01\tess_csf.mat
 
generating tetrahedral mesh from closed surfaces ...
creating volumetric mesh from a surface mesh ...

***************************************************************************
** Error: Line 52: 错误使用 readtetgen (line 52)
** wrong surface file
** 
** Call stack:
** >readtetgen.m at 52
** >surf2mesh.m at 121
** >process_fem_mesh.m>Compute at 384
** >process_fem_mesh.m>ComputeInteractive at 1226
** >process_fem_mesh.m at 32
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_fem_mesh,'ComputeInteractive',iSubject,[],GetAllFilenames(bstNodes)) at 1172
** 
***************************************************************************

Francois · February 14, 2022, 11:25am

@YRW
I can't download your files from here: 文件分享
It looks like we need a WeChat account, or something like that, which I don't have.
Please upload your file on a service that does not require to create any account.

YRW · February 14, 2022, 1:43pm

Sorry, I have re-uploaded [TutorialFem1_Subject01.zip] to GitHub, you can download the split volume compressed file.
https://github.com/Shuangquxian525/Brainstorm_proj

Francois · February 14, 2022, 6:04pm

Thanks.
I could reproduce the error on my computer (Win10).

@tmedani @tmedani @juangpc
This is exactly the tutorial... has it been tested on Windows?

dipole_9649.density = sparse 
dipole_9649.time = 0 
dipole_9650.density = sparse 
dipole_9650.time = 0.0010032 
Dune reported error: Dune::Exception [findEntityImpl:/home/juan/bst-duneuro/src/duneuro/duneuro/common/edgehopping.hh:84]: coordinate is outside of the grid, or grid is not convex 

status =
    -1

***************************************************************************
** Error: Error during the DUNEuro computation, see logs in the command window.
***************************************************************************

tmedani · February 15, 2022, 1:46am

yes we tested the pipeline on windows and its working.

@Francois just to make sure, are you using the mesh from simnibs or the mesh from iso2mesh?

I will check what is wrong on this data.

tmedani · February 15, 2022, 1:55am

@Francois did we fixed this error with the last discussion with iso2mesh dev team?

github.com/brainstorm-tools/brainstorm3

FEM tutorial: Issues to fix

opened 09:57AM - 13 Aug 21 UTC

ftadel

tutorials

1) **SimNIBS**: Remeshing the SimNIBS model with iso2mesh doesn't work. Here is …the error message: ``` FEM> 1. scalp: C:\Work\Protocols\TutorialFem\anat\Subject01\tess_scalp.mat FEM> 2. skull: C:\Work\Protocols\TutorialFem\anat\Subject01\tess_skull.mat FEM> 3. white: C:\Work\Protocols\TutorialFem\anat\Subject01\tess_white.mat FEM> 4. gray: C:\Work\Protocols\TutorialFem\anat\Subject01\tess_gray.mat FEM> 5. csf: C:\Work\Protocols\TutorialFem\anat\Subject01\tess_csf.mat generating tetrahedral mesh from closed surfaces ... creating volumetric mesh from a surface mesh ... *************************************************************************** ** Error: Line 117: surf2mesh (line 117) ** Tetgen command failed ** ** Call stack: ** >surf2mesh.m at 117 ** >process_fem_mesh.m>Compute at 442 ``` 2) **Pre-processing**: The PSD screen capture does not seem to be from this file (not the same time definition) 3) **Averaging**: The averaging screen capture shows a weighted average: this is confusing => Uncheck the "weighted" box 4) **Noise covariance**: - The name of the epochs in the screen capture is wrong ("2" and not "STI101") - The is a mention to a DC offset removal that was not applied when importing the epochs - The time window doesn't match between the text and the screen capture. 5) **Inverse model**: Redo screen captures with correct average file name. 6) **Dipole scanning**: - Redo screen capture to show only the LINKS (we can't select the shared kernels in Process1, as the text said before I edited it) - The dipole scanning process is executed over 40-60ms, but the results are illustrated at 21ms... - On my end, peak is at 22ms, not 21ms - If you scan the dipoles at multiple time points, you need to explain in the tutorial how to navigate in time and/or overlay multiple time points. Otherwise, simply scan at one specific time sample (eg. 21ms), this is simpler to display and post-process. - I find the second figure confusing. It should be split in two: in this section, show only the merge+renaming of the dipoles. Then make another figure to illustrate the dipoles display, and move it to the following section (P20/N20) 7) **Comparison: DTI vs isotropic**: - Add text to explain that you change the coloring of the dipoles "by group" - Explain how to change center the slices of the MRI 3D on a dipole (click on the dipole, the click on the "View/3D" button in the toolbar of the Dipole info panel) - "When we compare between the EEG and the MEG, there is a difference of 20mm between the localization between the MEG and the EEG": It looks less than 2cm in your screen captures... It would be worth illustrating how to compute this correctly: click on each dipole to see their locations (add screen capture of the dipole info panel), and compute the norm of the difference of the two vectors (`sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2)`) from the Matlab command line to get the exact distance (screen capture of the Matlab command window). - You need to explain the granularity of these results: you are using the cortex as the source space, the output of the dipole scanning can only be one of the vertices of the cortex surface. The two methods lead to the selection a selection of difference vertices, but it doesn't mean that there is "an error of XX millimeters" between the two methods. - "as well as a difference in the orientation in the coronal view": No, this difference in orientation is clearly visible in the three views. You can also compute the angle between the two from the orientation vector read in the dipoles info panel. 8) **Comparison: MEG vs EEG**: - "If we compare the difference between the EEG and MEG dipoles": Do you merge again the dipoles in a different way for this? If so, you need to tell the user to repeat the operation (possibly, this should be added in the previous section "Dipole scanning", as this is where you did the other merge). => Or you can keep the section but skip the figure , as it doesn't bring any additional interesting information (left and right figures look too similar) - I'm not sure what you can see here that you can't see in the in the previous figure. 9) **Comparison: FEM vs BEM**: - I get different plots than yours for EEG FEM DTI vs. EEG BEM: ![image](https://user-images.githubusercontent.com/6920058/129355933-e4f7c603-1a93-47e2-8b9c-0369cc52bf19.png) ![image](https://user-images.githubusercontent.com/6920058/129355979-02d4fd32-29b5-4e59-b0ce-992aa14b7403.png) ![image](https://user-images.githubusercontent.com/6920058/129356033-1a74859a-ddef-49fc-b2af-8630b04a5952.png) 10) **DUNEuro advanced options**: Merged into the DUNEuro tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro#DUNEuro_options:_Advanced_.5BTODO.5D => Must be edited, most options are not documented. 11) Removed text (too drafty): "Dipoles outside of the grid for the MEG: remove this dipole or replace it with its spatial neighbors (not the neighbor in the list) ==> not easy to handle write small tuto? " 12) Review associated FEM tutorials (Francois): - https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro => **DONE** - Documentation of all the advanced options missing: - https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors => **DONE** - https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh => **DONE** - Iso2mesh: Removed link "From our test", which was pointing at https://neuroimage.usc.edu/brainstorm/reviewMEEGForward?highlight=(duneuro), which does not exist. - Juan, Takfarinas: Please have a look to make sure that it still looks like what you wanted.

I believe that the error is due to some hole on the mesh, but I will check it again.

Francois · February 16, 2022, 5:59pm

It is the mesh from SimNIBS, that @YRW posted on github.

@Francois did we fixed this error with the last discussion with iso2mesh dev team?

Yes, I believe it was fixed.
At least it works now on my Win10 computer:

@YRW
Takfarinas is right, you haven't gone through the step of remeshing the SimNIBS mesh.
It is clearly stated in the tutorial that in case of problem with MEG and SimNIBS meshes with air cavities, you must remesh the layers.
Please follow this section step by step:
https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve#Remesh_with_Iso2mesh

If you have issues with iso2mesh, please post full error messages and screen captures.

YRW · February 18, 2022, 1:49am

But when I remesh the layers with iso2mesh, error occur

***************************************************************************
** Error: Line 398: The index at position 1 is invalid.  The array index must be a positive integer or logical value 
** 
** Call stack:
** >process_fem_mesh.m>Compute at 398
** >process_fem_mesh.m>ComputeInteractive at 1226
** >process_fem_mesh.m at 32
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_fem_mesh,'ComputeInteractive',iSubject,[],GetAllFilenames(bstNodes)) at 1172
** 
***************************************************************************


***************************************************************************
** Error: The FEM mesh generation failed.
** Check the Matlab command window for additional information.
** 
***************************************************************************

YRW · February 18, 2022, 1:51am

Can you send the file "FEM 679613V (iso2mesh-2021, 5layers)" to me, thank you every much

Francois · February 18, 2022, 5:48pm

But when I remesh the layers with iso2mesh, error occur

Are your versions of Brainstorm and Iso2mesh up-to-date? - Maybe try to update both.
I've been running this computation from your database... we're both on Win10 so I don't see why the results of Iso2mesh would be different...
What is your version of Matlab?
Are your sure your followed exactly the instructions from the tutorial?

Can you send the file "FEM 679613V (iso2mesh-2021, 5layers)" to me, thank you every much

Here it is: Dropbox - File Deleted - Simplify your life

But I'd prefer you keep on trying computing it on your own... At least to help us debug completely this issue

YRW · February 25, 2022, 12:53pm

thank you very much

YRW · March 14, 2022, 1:43am

thank you, I have download your "FEM 679613V(iso2mesh-2021)", when I used it to compute ISO MEG head model, it worked. But when I used it to compute DTI MEG head model, error occur

dipole_2987.density = sparse 
dipole_2987.time = 0 
Dune reported error: Dune::Exception [findEntityImpl:/home/juan/bst-duneuro/src/duneuro/duneuro/common/edgehopping.hh:84]: coordinate is outside of the grid, or grid is not convex 

status =

    -1


***************************************************************************
** Error: Error during the DUNEuro computation, see logs in the command window.
***************************************************************************

Francois · March 14, 2022, 10:19am

I have download your "FEM 679613V(iso2mesh-2021)"

I strongly advise you compute this file yourself instead of using the one I posted, in order to debug all the processing chain upstream and validate the contents of your database. If you have errors in other files, it is pointless for us to try and debug the problems you report.

when I used it to compute ISO MEG head model, it worked. But when I used it to compute DTI MEG head model, error occur

It seems unlikely that DUNEuro would check for the grid in the anisotropic case, but not in the isotropic case. Please check again what you are doing.

@tmedani @juangpc ?

YRW · March 15, 2022, 12:27pm

I did try to remesh with Iso2mesh as tutorials say, but error occur

Then we need to do further debugging, please share the following information:

Zip together: the MRI file + the surface files you select in the subject anatomy folder in order to obtain this error
Upload the .zip file somewhere and post the download link here (please try using an appropriate service for that, not github, if you can find one that does not require a WeChat account...)
Post the screen capture of the window you get with the menu "Plugins > List" in Brainstorm.

Failed to save the desktop configuration

This is not coming from Brainstorm.
You have additional configuration issues on your computer.

***************************************************************************
** Error: Line 39: incorrectly use of readtetgen (line 39)
** wrong elem file
** 
** Call stack:
** >readtetgen.m at 39
** >surf2mesh.m at 121
** >process_fem_mesh.m>Compute at 384
** >process_fem_mesh.m>ComputeInteractive at 1226
** >process_fem_mesh.m at 32
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_fem_mesh,'ComputeInteractive',iSubject,[],GetAllFilenames(bstNodes)) at 1172
** 
***************************************************************************

Failed to save the desktop configuration

***************************************************************************
** Error: The FEM mesh generation failed.
** Check the Matlab command window for additional information.
** 
***************************************************************************