Hi, I was trying to reproduce Locating Intracranial Electrode Contacts — MNE 0.24.0 documentation, and the first step is aligning the T1 to ACPC. I did locating using brainstorm before, I’m not sure it has this step using brainstorm. And may I ask why? For I see some tutorials about freesurfer, it seems that they don’t need this step.
And from the tutorial, does it mean that I should do the alignment manually using my mouse?
From the tutorial, is seems that I should move the mouse to the wanted center and click the button in the translate module.
Aligning to ACPC does not effect the analysis itself, the purpose is that ACPC is the recommended coordinate frame for ieeg in BIDS (scanner RAS is also acceptable now but ieeg folks like to compare datasets in ACPC so we left this in as a recommendation).
Thank you so much for your reply. So if I just locate the electrodes, it’s OK that I directly do recon-all -i *** -sd *** -all.
Also how do I know __ change those sliders with the RAS (NB RAS not TKreg RAS )___?
Yes, you can skip the ACPC alignment step, everything will work fine subsequently. The only caveat is that when you get to the very end and want to put your data in BIDS, you would have to do the whole preprocessing over again starting with the ACPC alignment so it’s generally a good idea to do it.
NB means nota bene and it’s latin for note well which I used just to say be careful because RAS and TKReg RAS are right next to each other and setting the wrong one won’t actually align to ACPC (you want RAS). You change the sliders until all the windows look like those in the reference and the plots in the tutorial (i.e. center on AC, passing through the PC, eyes the same size and aligned to midline).
