My name is Rachel. I am new to BrainStorm. I am working on sEEG recordings.
(1) I downloaded a pubic sEEG recordings online. This patient's MRI and CT are provided in .nii format and co-registered to the Talairach coordinate space. The eye area is covered with black strip. So after I import the MRI in brainstorm, I cannot set the NAS/LPA/RPA. I have the channel_file. I want to generate a forward model with the data I have. The tutorials I read all require NAS/LPA/RPA points to proceed. Am I able to generate a forward model with what I have?
(2) I am also trying to build a simple simulation of sEEG setup. I use the template "MRI: ICBM152" anatomy. And I choose some sEEG electrode positions by hand(I make sure the positions are inside the cerebrum.) And I run 'compute head model'. And I got the error below.
The coordinates you want to import are in Talairach coordinates, so you wouldn’t be able to import them on the patient’s MRI even if you had the NAS, LPA and RPA points.
I added last week the possibility to import the position of SEEG contacts in MNI space. You should start by updating Brainstorm to make sure you have this last version on your computer (menu Help > Update Brainstorm).
Can you have access to these coordinates in MNI space, or can you convert them from Talairach to MNI? (the two reference systems are similar but have a different origin and a slight scaling problem - Talairach coordinates system is an outdated system, even though still widely used in hospitals)
Yes, you should be able to compute forward and inverse models once the coordinates of the SEEG contacts are registered properly with the MRI of the subject.
But note that the SEEG electrodes record very local potentials, it is not possible to infer correctly what is happening in the rest of the brain with such a sparse sampling. The source estimation based on SEEG recordings seems somewhat artificial to me. It should not produce very different results from the simple re-interpolation of the SEEG recordings in the MRI (not available in Brainstorm yet).
If you have questions about this approach, please contact the developers of the software OpenMEEG: http://neuroimage.usc.edu/brainstorm/Tutorials/TutBem
Can you let us know where you got this data from? This could be an interesting possibility for a new Brainstorm SEEG tutorial.
This is a question for the OpenMEEG developers. I will forward them your question.
I guess you are talking about this tutorial: http://www.fieldtriptoolbox.org/tutorial/human_ecog
We will have a look at it, it would be interesting to have a Brainstorm tutorial that replicates these results (but it may not happen before the summer…)
In the meantime, let me know if you have questions about the other information I posted.
Could you package an example dataset for us to test?
Duplicate the subject for which you are getting this error (right-click on the subject folder > File > Duplicate subject)
Delete all the files that are not necessary to reproduce the error (both in the anatomy and the functional sides of the protocol, keep only the MRI, the head surface and the cortex surface that is selected), to make the file easier to share
Right-click on the subject > File > Export subject
Upload the .zip somwhere (eg. dropbox) and send me link by email (click on my username on this forum)
I will repackage the data so that it can be tested easily with different versions of OpenMEEG.
Thank you for the example file. I tested it on my windows 10 laptop and it works correctly.
I right-click on the the channel file > Compute head model > Use all the default parameters, and it creates correctly the forward model.
Maybe this is a bug specific to your operating system?
Please copy-paste the output of the “ver” command in Matlab in this thread, and I will try to test it on a similar OS.
If you are using the compiled Matlab version, please report the name and version of your operating system and the version of Matlab.
Thank you for looking into this.
I also tested on a Mac, and it didn’t work. Below is my output of ver.
MATLAB Version: 9.0.0.341360 (R2016a)
Operating System: Microsoft Windows 10 Home Version 10.0 (Build 14393)
Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot™ 64-Bit Server VM mixed mode
MATLAB Version 9.0 (R2016a)
Simulink Version 8.7 (R2016a)
Bioinformatics Toolbox Version 4.6 (R2016a)
Communications System Toolbox Version 6.2 (R2016a)
Computer Vision System Toolbox Version 7.1 (R2016a)
Control System Toolbox Version 10.0 (R2016a)
Curve Fitting Toolbox Version 3.5.3 (R2016a)
DSP System Toolbox Version 9.2 (R2016a)
Data Acquisition Toolbox Version 3.9 (R2016a)
Database Toolbox Version 6.1 (R2016a)
Embedded Coder Version 6.10 (R2016a)
FieldTrip Version unknown fieldtriptoolbox.org
Financial Instruments Toolbox Version 2.3 (R2016a)
Financial Toolbox Version 5.7 (R2016a)
Fixed-Point Designer Version 5.2 (R2016a)
Fuzzy Logic Toolbox Version 2.2.23 (R2016a)
Global Optimization Toolbox Version 3.4 (R2016a)
HDL Coder Version 3.8 (R2016a)
HDL Verifier Version 5.0 (R2016a)
Image Acquisition Toolbox Version 5.0 (R2016a)
Image Processing Toolbox Version 9.4 (R2016a)
Instrument Control Toolbox Version 3.9 (R2016a)
MATLAB Coder Version 3.1 (R2016a)
MATLAB Compiler Version 6.2 (R2016a)
MATLAB Compiler SDK Version 6.2 (R2016a)
Mapping Toolbox Version 4.3 (R2016a)
Model Predictive Control Toolbox Version 5.2 (R2016a)
Model-Based Calibration Toolbox Version 5.1 (R2016a)
Neural Network Toolbox Version 9.0 (R2016a)
Optimization Toolbox Version 7.4 (R2016a)
Parallel Computing Toolbox Version 6.8 (R2016a)
Partial Differential Equation Toolbox Version 2.2 (R2016a)
RF Toolbox Version 3.0 (R2016a)
Robotics System Toolbox Version 1.2 (R2016a)
Robust Control Toolbox Version 6.1 (R2016a)
Signal Processing Toolbox Version 7.2 (R2016a)
SimEvents Version 5.0 (R2016a)
SimRF Version 5.0 (R2016a)
Simscape Version 4.0 (R2016a)
Simscape Driveline Version 2.10 (R2016a)
Simscape Electronics Version 2.9 (R2016a)
Simscape Fluids Version 2.0 (R2016a)
Simscape Multibody Version 4.8 (R2016a)
Simscape Power Systems Version 6.5 (R2016a)
Stateflow Version 8.7 (R2016a)
Statistics and Machine Learning Toolbox Version 10.2 (R2016a)
Symbolic Math Toolbox Version 7.0 (R2016a)
System Identification Toolbox Version 9.4 (R2016a)
Wavelet Toolbox Version 4.16 (R2016a)
Hi Francois,
Thanks for looking into this. I realize I had an error because I chose “using adjoint formulation” before. The “adaptive integration” works fine for both cortex source and MRI volume source for Ecog and sEEG electrodes.
Thank you for this information.
It was the combination of ECOG and this adjoint option that was not handled well in Brainstorm.
I fixed it, you should be able to use it after updating Brainstorm (but you don’t really need this option if the other approach works, they give the same results).
FYI: We improved significantly the tools available in Brainstorm for processing and visualizing SEEG and ECOG data, including new options for volume coregistration. They are now documented in a new tutorial: http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity
