I want to get the talairach coordinates MEG sensors using the cs_scs2tal function. However, I don’t know how to define the CortexVert matrice (cs_scs2tal.m file describes it as a “3xN matrix containing the SCS coordinates of the vertices of the tessellation”). What does it mean and how can find these informations?
Besides, my other variables are defined as follows:
Please ignore this “talairach” coordinates in the GUI, and do not use this function. The results given by cs_scs2tal are wrong and will be removed from Brainstorm before the end of the year. Unless the authors really want to fix it…
Besides, the “talairach” coordinates are a normalized system to designate brain regions, and may not be used to point at anything that is outside of the head. Does that make sense?
For sure, it makes sense that this function does not make sense!
However, I would like to select the MEG sensors recording the activity of a ROI defined by its Talairach barycenter, in order to measure their CTF activity, via dataHandler. Do you know how I could find these sensors?
Has this issue been resolved? I would like to define an ROI scout based on MNI or Talairach coordinates but do not see a transform between either of these coordinate systems and Brainstorm’s default Colin template.
The Talairach coordinates that were displayed previously in the Brainstorm interface were wrong. I removed them a few months ago.
We will work at some point on a new default anatomy using the recent works in brain normalization, that will provide a correspondence with the MNI space.
But this is not a high priority and will probably not happen before the end of the year, sorry.
Hey Francois ~ Following on this thread, could you advise me on the recommended method for creating scouts? If you do not have a recognized coordinate system to report - do you have an alternate method that you use?
Many thanks!
Agatha
I finally fixed the MNI coordinates display in the MRI viewer and the “Coordinates” window (right-click on a 3D figure > Get coordinates").
It gives accurate values on the default anatomy in Brainstorm (as the Colin27 brain is used as a reference for the MNI coordinates).
For individual brains, it does a basic scaling do match the size of the Colin27 brain, but do not expect this to be very accurate. To get slightly better MNI coordinates, you can re-project the sources on the Colin brain and then get the coordinates.
Ah fantastic. Thanks for adding in this so quickly - this will make the outputs of Brainstorm much much more accessible to the ‘outside’ world. BTW - the atlas has worked quite well for me. It’s definitely user friendly. Thanks on both accounts. Agatha
I am trying to extract SCS scouts coordinates and convert them to Talaraich coordinates.
I read in this topic that the script “cs_scs2tal.m” was not working properly.
Following the topic, I get that the “get coordinates” from the GUI is already fixed in the last versions of brainstorm and I would like to know if the script “cs_scs2tal.m” is also fixed.
I use this script and the outputs correspond to the ones I observed in the “get coordinates” from the GUI under the label MNI. Is this correct? Because I was expecting that Talaraich coordinates to be different from the MNI coordinates.
There is no support for the Talaraich coordinates anymore. This function cs_scs2tal is just used for aligning different cortex surfaces along the AC/PC axis, you shouldn’t try to use it manually.
You can have access to the MNI coordinates in the MRI Viewer and the “Get coordinates” windows in the 3D figures (right-click on the figure that contains a cortex).
As said before in this thread: for individual brains, it does a basic scaling to match the size of the Colin27 brain, but do not expect this to be very accurate. To get better MNI coordinates, you can re-project the sources on the Colin brain and then get the MNI coordinates.