Dear all,
I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images.
Best, Xiangyu
Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long longspace82@gmail.com wrote:
Dear all,
I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images.
Best, Xiangyu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Allison, however, I checked the website and it is said that FreeSurfer transform the orig volume to the MNI305 atlas, so the spatial normalization in FreeSurfer is still done in volume space but not in surface space, right?
Best, Xiangyu
On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player < astevens@nmr.mgh.harvard.edu> wrote:
Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long longspace82@gmail.com wrote:
Dear all,
I had EPI images and T1 image and the EPI images are already
co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images.
Best, Xiangyu _______________________________________________ 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.
I'm sorry, I misunderstood. This website may be more helpful:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration
On Feb 24, 2012, at 10:39 AM, Long longspace82@gmail.com wrote:
Thank you Allison, however, I checked the website and it is said that FreeSurfer transform the orig volume to the MNI305 atlas, so the spatial normalization in FreeSurfer is still done in volume space but not in surface space, right?
Best, Xiangyu
On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player astevens@nmr.mgh.harvard.edu wrote: Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
On Feb 22, 2012, at 11:26 AM, Long longspace82@gmail.com wrote:
Dear all,
I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images.
Best, Xiangyu _______________________________________________ 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@nmr.mgh.harvard.edu
-
Allison Stevens Player -
Long