Thanks Bruce.
Okay will convert them from scanner RAS to surface RAS; 
last question: I looked at the control points made from tkmedit; 
it seems like you round of the co-ordinates to integers and then save them as floats;
Does the co-ordinate information saved in control.dat need to be rounded 
or is it okay to save floats in control.dat; ?

I also noticed the following difference between tkmedit and freeview; 

if I make and save control points in tkmedit it says "useRealRAS 0"
while if i make and save control points in  freeview it says "useRealRAS 1" (here the co-ordinate info is not rounded off). Not sure if this could affect the workflow but just wanted to let you know; 

Thanks
Mehul

ps: In case, anyone needs to convert from scanner RAS to surface RAS; this is how I am doing it in Matlab:

1. First read the vox2ras0 from MRIread and compute it's inverse. 
2. Then do a matrix multiplication to get surface RAS. that is:
surface RAS = inv(vox2ras0) * scanner RAS;

Mehul


On Mon, Jul 1, 2013 at 12:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
1. Yes, I think so, although I wouldn't swear that everything is smart enough to read this flag. You might be safer converting them to surface ras and using them that way

2. Yes.


On Mon, 1 Jul 2013, Mehul Sampat wrote:

Thanks Bruce; Okay i assume, useRealRAS should be 1 for scanner RAS; 
Two questions: 
1. If my control points are in scanner RAS, then can I use them directly as
long as I set 
useRealRAS to 1 in the control.dat file ?
2. Can useRealRAS variable be only 0/1 or do you have a different value for
surface RAS?

Thanks
Mehul




On Mon, Jul 1, 2013 at 12:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Mehul

      they can either be in "real" (meaning scanner) RAS or in surface
      RAS

      cheers
      Bruce
      On Mon, 1 Jul 2013, Mehul Sampat wrote:

            Thanks Bruce; I noticed that in the control.dat file
            the second last line is
            "useRealRAS 0"
            just curious to know if info is used by recon-all or
            is only used by the
            viewer ? 
            Thanks
            Mehul


            On Mon, Jul 1, 2013 at 11:34 AM, Bruce Fischl
            <fischl@nmr.mgh.harvard.edu>
            wrote:
                  yes, they are stored in ras
                  On Mon, 1 Jul 2013, Mehul Sampat wrote:

                        Hi Folks, Once we make control points in
            tkmedit,
                        they are stored in the
                        file control.dat
                        Are these control points stored in RAS
            co-ordinate
                        system ?
                        If not what is the co-ordinate system
            used to store
                        the control points
                        Thanks
                        Mehul





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