Dear all,
I need to transform my electrode FS volume index coordinates stored in a .mat file (see attached) in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates?
Thank you,
Octavian Lie.
Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie.
*To follow up and simplify for a single electrode location, * ** *What I need to do is for each electrode (already localized/ projected onto the surface) to transform its volume volume index coordinate to a vertex RAS (maybe via the closest vertex volume coordinates), then to transform these vertex RAS coordinates to fsaverage template coordinate.* *I then need to calculate the geodesic and euclidean distance between the electrode location and another selected surface vertex, say (a,b,c).* *Thank you for your insight.* ** *Octavian Lie.*
Hi Octavian, these types of things are generally not difficult to program, but they can be difficult to get set up correctly. If you do a search for "coordinates" on our wiki, it will take you to a page that explains the process. doug
On 09/26/2012 02:57 PM, octavian lie wrote:
Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. *To follow up and simplify for a single electrode location, * ** *What I need to do is for each electrode (already localized/ projected onto the surface) to transform its volume volume index coordinate to a vertex RAS (maybe via the closest vertex volume coordinates), then to transform these vertex RAS coordinates to fsaverage template coordinate.* *I then need to calculate the geodesic and euclidean distance between the electrode location and another selected surface vertex, say (a,b,c).* *Thank you for your insight.* ** *Octavian Lie.*
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Sorry, I do not seem to see the light. I have a point in volume index coordinates [128.9 172 62.9 1] and need to obtain the surface/vertex RAS coordinates (not volume RAS).
matlab path /usr/local/freesurfer/subjects/subjid/mri if I type tkrRAS = Torig*[128.9 172 62.9 1]'
it tells me Torig undefined function or variable
If I try to define it with Torig: mri_info --vox2ras-tkr orig.mgz, it does not recognize mri_info
Nothing happens if I work from the freesurfer command window:
- Torig = mri_info --vox2ras-tkr orig.mgz
- tkrRAS = Torig*[128.9 172 62.9 1]'
I do not want to use tkmedit/tksurfer clicking since I plan doing this transform for a list of points.
I know this is boringly basic but I am stuck, please advise.
Octavian
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