[Freesurfer] MNI305 coordinates to RAS
I am trying to convert MNI305 coordinates to RAS. I have only been able to find a way to find MNI305 from RAS but not the other way around: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' from http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemshttp://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems Is there a known equation with transforms to go from MNI to RAS? Thanks, Juan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] MNI305 coordinates to RAS
Hi Bruce, The problem is that it TalXFM is a 3x4 matrix. It needs to be a square matrix to be inverted. Juan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, January 29, 2015 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] MNI305 coordinates to RAS Hi Juan if you invert that matrix it will go the other direction cheers Bruce On Thu, 29 Jan 2015, Diaz Rodriguez, Juan wrote: > I am trying to convert MNI305 coordinates to RAS. I have only been able to > find a way to find MNI305 from RAS but not the other way around: > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' from > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemshttp://surfer.nmr > .mgh.harvard.edu/fswiki/CoordinateSystems > > Is there a known equation with transforms to go from MNI to RAS? > > Thanks, > > Juan > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] MNI305 coordinates to RAS
Hi Bruce, It worked! thank you. Juan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, January 29, 2015 3:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] MNI305 coordinates to RAS Hi Juan add a 4th row that is [0 0 0 1], then invert it cheers Bruce On Thu, 29 Jan 2015, Diaz Rodriguez, Juan wrote: > Hi Bruce, > > The problem is that it TalXFM is a 3x4 matrix. It needs to be a square matrix > to be inverted. > > Juan > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, January 29, 2015 3:33 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] MNI305 coordinates to RAS > > Hi Juan > > if you invert that matrix it will go the other direction > > cheers > Bruce > On Thu, 29 Jan > 2015, Diaz Rodriguez, Juan wrote: > >> I am trying to convert MNI305 coordinates to RAS. I have only been able to >> find a way to find MNI305 from RAS but not the other way around: >> MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' from >> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystemshttp://surfer.nmr >> .mgh.harvard.edu/fswiki/CoordinateSystems >> >> Is there a known equation with transforms to go from MNI to RAS? >> >> Thanks, >> >> Juan >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Creating ROI
I am trying to create a spherical ROI mask in the form of a volume file with 2.5 cm radius. I also have to specify the center of the ROI location. What is the best way to accomplish this? I intend to use this to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space as described in https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
