I moved this post to a new thread.
Please create a new thread for each new question or bug report.
it would help to have the software automatically localize the artifact and attempt to make SEEG contacts that I can then modify instead of individually going through post-implant CT and marking them manually.
At this moment, Brainstorm doesn't include any solution for automated SEEG contact identification.
There are semi-automated methods available (e.g. GARDEL:presentation - WikiMEG) but we haven't tested them or integrated them with Brainstorm yet. This will be part of the developments of the next few years.
#Anatomical_labelling section shows a way to use an atlas to automatically place SEEG electrodes, but the option does not appear on my subject channel file.
There are no tools in Brainstorm to place SEEG electrodes automatically.
The sections "Anatomical labelling" in the SEEG and the ECOG tutorials explain how to export as a table the labels of the anatomical regions in which the existing SEEG contacts are located.
The recorded data I have channel file marks the type of recordings as EEG when in fact they are SEEG recordings. Does that make a difference?
Yes, you need to edit the channel file to change the type of the channels.
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Prepare_the_channel_file
In another test subject I tried to make a SEEG implant and manually entered locations of electrodes entry/target and then exported positions as .pol file, then I right click channel file then add electrode positions and import the .pol file.
This seems unnecessarily complicated.
Link your SEEG recordings to the database, edit the channel file to mark the channels as SEEG, then edit the positions as explained in the tutorials.
I once edited the SEEG implant by adjusting an electrdoe, then all the positions became removed outside of the skull in same reference to each other, but not in reference to CT or MRI.
I'm not sure I understand what this means.
The channel file also has the problem that the channels are grouped only as one group E. I can go through and edit the groups to reflect individual channels. Would that help?
Yes, edit the groups of the channels manually.
If the electrodes are all identified as part of the group "E", they all start with the letter "E".
The SEEG tools in Brainstorm will work only if your channels are labelled following the widely used conventions of having each SEEG shaft represented with a letter (e.g. "A") and the contacts along this shaft numbered from 1 to n, 1 being the deepest contact (e.g. A1, A2, ..., An).
Immediately after linking your recordings to the database: you can edit the channel file and rename the channels to match this convention.
Or must I still go and manually select entry and target points for each electrode?
You need to do both. Set the groups/names first, then define the position of the electrodes.