Hi John, please remember to post to the list. thanks! Yes, that should work. Use read read_surf.m to get the proper coordinates. doug

On 04/20/2014 08:08 PM, John Pyles wrote:

Hi Doug,

Thanks so much for the reply.

I had looked through the wiki on coordinates but because I'm not a big Freesurfer user was unsure which was the correct transformation.

It seems like for what I need to do the example below is appropriate? So in theory I could write a Matlab function using the calculation below correct?

Thanks again.

Best, John

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2. I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS"

from tksurfer) and want to compute the MNI305 RAS that corresponds to this point:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'

TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info

--vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz

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John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpyles@cmu.edu phone: 206.552.0107 ______________________________________

On Fri, 18 Apr 2014, Douglas Greve wrote:

...

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).

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

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John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University ______________________________________

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