Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There's also a wiki page on how to do this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
Bruce Fischl wrote:
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ 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
Hi,
I actually have a MPRAGE and a chemical shift imaging data (both shifted and rotated from isocenter) and I would like to register the mprage according to the header of the csi data. Is there an easy way to do this?
Cheers, Trina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
There's also a wiki page on how to do this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
Bruce Fischl wrote:
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
what is the resolution of the CSI image? Was it and the mprage acquired in the same session? On Sun, 29 May 2011, Trina Kok wrote:
Hi,
I actually have a MPRAGE and a chemical shift imaging data (both shifted and rotated from isocenter) and I would like to register the mprage according to the header of the csi data. Is there an easy way to do this?
Cheers, Trina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
There's also a wiki page on how to do this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
Bruce Fischl wrote:
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Yup they are acquired in the same session, so it's just the rotation and isocenter that's different. The CSI image has a different resolution ard 0.8cc.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
what is the resolution of the CSI image? Was it and the mprage acquired in the same session? On Sun, 29 May 2011, Trina Kok wrote:
Hi,
I actually have a MPRAGE and a chemical shift imaging data (both shifted and rotated from isocenter) and I would like to register the mprage according to the header of the csi data. Is there an easy way to do this?
Cheers, Trina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
There's also a wiki page on how to do this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
Bruce Fischl wrote:
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
then you should be able to use -regheader in tkregister2 to get close (or use -initheader in bbregister)
On Mon, 30 May 2011, Trina Kok wrote:
Yup they are acquired in the same session, so it's just the rotation and isocenter that's different. The CSI image has a different resolution ard 0.8cc.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
what is the resolution of the CSI image? Was it and the mprage acquired in the same session? On Sun, 29 May 2011, Trina Kok wrote:
Hi,
I actually have a MPRAGE and a chemical shift imaging data (both shifted and rotated from isocenter) and I would like to register the mprage according to the header of the csi data. Is there an easy way to do this?
Cheers, Trina
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
There's also a wiki page on how to do this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
Bruce Fischl wrote:
Hi Trina
you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then
R1 * inv(R2)
cheers Bruce
p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do.
On Mon, 23 May 2011, Trina Kok wrote:
Hi All,
We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below.
[orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension];
On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space?
Thanks a lot!
Cheers, Trina _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Trina Kok