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
______________________________________
John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University ______________________________________
There is not a simple function, but you can look at our wiki page on coordinate systems. There are some examples there on tranforming from one coordinate to another doug
On 4/18/14 2:40 PM, John Pyles wrote:
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).
- 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
John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University ______________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
John Pyles