ACPC alignment about T1

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.

Thank you

I’m tagging @alexrockhill here, who created this Interface

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).

Looks like you are on the right track from your screenshots, you just change those sliders with the RAS (NB RAS not TKreg RAS) locator box at the bottom of the screen set to (0, 0, 0) until it looks like the figure in the tutorial that is ACPC aligned. The process is described in detail here Frontiers | Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography | Frontiers in Neuroinformatics.

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).

Actually writing this, it looks like Figure 3 from the reference ( has the brain facing the wrong way so I would recommend not doing that. According to this How are the different head and MRI coordinate systems defined? - FieldTrip toolbox and Coordinate systems - Brain Imaging Data Structure v1.6.0. The brain/face should face right.
You can take a try with acpcdetect.

Thank you for your recommendation!

Hi, may I ask how do you use acpcdetect usually.

acpcdetect -i *.nii


这个软件有个pdf的manual 可以看看manual 里面讲的很详细
acpcdetect -v -center-AC -i xxx.nii


看手册说的 -center-AC就是把原点设置在AC是吗,感觉和教程说得一致。