Hi Francois,
I am trying to figure out how to obtain the SEEG coordinate (x, y, z list). I have the coordinate from a colleague and she obtained it from the T1-contrast image of a patient which I assume is in world template.
However I need to work on the T1 non-contrast image (from the same patient), however I am not sure if I can extract the new coordinate list from Brainstorm after I co-registered T1 non-contrast to T1-contrast and put the SEEG coordinate on the co-registered images? Is there a way to do that?
Thank you,
Jacob
From the interface: right-click on the channel file in which the positions of the SEEG contacts are defined > Display > Select the MRI volume you want. Then navigate in the volume and read the "world" coordinates for this volume.
If you are expecting to use a Matlab script to get the positions of SEEG contacts that are already visible in the Brainstorm MRI viewer in the scanner-based coordinates (= world coordinates) of one of the volumes imported and co-registered in the subject anatomy folder, you can do the following:
- Right-click on the channel file > File > Export to Matlab > "ChannelMat"
- Get the SCS coordinates of all the contacts:
P_scs = [ChannelMat.Channel.Loc]'
- Right-click on the MRI in which you want the coordinates > File > Export to Matlab > "sMri"
- Convert the coordinates from SCS to WORLD coordinates:
P_world = cs_convert(sMri, 'scs', 'world', P_scs);
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems
If this does not answer your question, please describe more precisely your objectives, including screen captures.