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
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
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.eduwrote:
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 MehulThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.eduwrote:
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 MehulThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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:
- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.eduwrote:
- 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
- Yes.
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce; Okay i assume, useRealRAS should be 1 for scanner RAS;
Two questions:
- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mehul
writing as full floats should be fine, I didn't realize tkmedit rounded Bruce
On Mon, 1 Jul 2013, Mehul Sampat wrote:
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:
- First read the vox2ras0 from MRIread and compute it's inverse.
- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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