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
>
>
> ------------
> 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
> ------------
>
>
> ______________________________________
>
> John Pyles, Ph.D.
> Research Scientist
> Center for the Neural Basis of Cognition
> Department of Psychology
> Carnegie Mellon University
> email: jpy...@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
>>
>> ______________________________________
>>
>> 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
>>
>>
>>
>>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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