Hi,
I am not a heavy Freesurfer user and I haven't had good
luck figuring this out through the FreeSurfer documentation
and I thought an expert might have a fast answer. If anyone
has an easy solution it would be very much appreciated.
While I use FreeSurfer for automatic segmentation, I don't
normally use if for analysis. However for an ECoG project I'm
using parts of FreeSurfer to aid in electrode coregistration.
Basically the issue is that I have electrode coordinates in
what I believe are FreeSurfer RAS space and I need to convert
them to MNI space. I have many of these electrode coordinates
for each subject so I need a FreeSurfer or Matlab function to
automate this process. Is there a simple way to do this?
The *very* kludgy way I figured out how to do this
"manually" is as follows (I'm sure this is going to seem very
dumb to a FreeSurfer user, but I needed a quick solution that
worked for a figure).
1) Enter the coordinate output from my electrode
coregistration routines manually into the RAS field in
Freeview.
2) Take the "brain volume" coordinates (all positive) in
Freeview and enter them into the "Volume Coordinate" field in
TkMedit.
3) Copy the TAL coordinates output in MkEdit when the brain
volume coordinate is entered.
4) Convert the TAL coordinates to MNI in Matlab with
tal2mni.m
It seems like there should be a simple function to do this
coordinate conversion using the transformation info from
recon-all that I'm assuming both Freeview and TkMedit use, but
I can't seem to find it?
Any help would be appreciated. Thanks again!
Best,
John