To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath
Hi Garrett-
Ziad wrote a program for AFNI (@SUMA_Make_Spec_FS) which converts all .mgz files to nifti format using Freesurfer's mri_convert. I believe there is also an AFNI program @SUMA_FSvolToBRIK which may do what you want? The AFNI message board has some information on this, although mri_convert in Freesurfer may do what you want (not sure if it preserves the transformation though...
Anthony
Garrett McGrath wrote:
To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think you can use mri_vol2vol to apply the register.dat created by tkregister2.
cheers, Bruce On Fri, 15 Feb 2008, Anthony Dick wrote:
Hi Garrett-
Ziad wrote a program for AFNI (@SUMA_Make_Spec_FS) which converts all .mgz files to nifti format using Freesurfer's mri_convert. I believe there is also an AFNI program @SUMA_FSvolToBRIK which may do what you want? The AFNI message board has some information on this, although mri_convert in Freesurfer may do what you want (not sure if it preserves the transformation though...
Anthony
Garrett McGrath wrote:
To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks all for the responces, I'll give these things a try.
Bruce Fischl wrote:
I think you can use mri_vol2vol to apply the register.dat created by tkregister2.
cheers, Bruce On Fri, 15 Feb 2008, Anthony Dick wrote:
Hi Garrett-
Ziad wrote a program for AFNI (@SUMA_Make_Spec_FS) which converts all .mgz files to nifti format using Freesurfer's mri_convert. I believe there is also an AFNI program @SUMA_FSvolToBRIK which may do what you want? The AFNI message board has some information on this, although mri_convert in Freesurfer may do what you want (not sure if it preserves the transformation though...
Anthony
Garrett McGrath wrote:
To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can use mri_vol2vol to convert the input volume to the output space (ie, reslice), or you can use the --no-resample option to keep it in it's native space and just change the qform/sform matrix (sounds like what you want).
doug
On Fri, 15 Feb 2008, Garrett McGrath wrote:
To the freesurfer people: I would like to know if there is a way to generate a new volume file from the original volume file using the matrix of transformations generated by tkregister. I need to be able to transport those changes over to afni which lacks the nice interface freesurfer has for registration. Is there currently a way to do this? or an easy way to convert those values into something usable by afni? -Garrett McGrath _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Anthony Dick -
Bruce Fischl -
Doug Greve -
Garrett McGrath