Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote:
Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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.
Hi Thomas,
I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas?
Thanks,
Ting
On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote:
Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register
the
functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ting,
What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future.
The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this.
Cheers, Thomas
On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutingxt@gmail.com wrote:
Hi Thomas,
I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas?
Thanks,
Ting
On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote:
Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for your reply with detailed explanation. I am interested in what if we apply analysis on native surface first. Still wondering:)
Ting
On Nov 23, 2014, at 8:23 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future.
The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this.
Cheers, Thomas
On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutingxt@gmail.com wrote: Hi Thomas,
I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas?
Thanks,
Ting
On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote: Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Would mris_decimate work?
On 11/24/2014 01:53 AM, 婷 wrote:
Thanks for your reply with detailed explanation. I am interested in what if we apply analysis on native surface first. Still wondering:)
Ting
On Nov 23, 2014, at 8:23 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future.
The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this.
Cheers, Thomas
On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutingxt@gmail.com wrote: Hi Thomas,
I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas?
Thanks,
Ting
On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote: Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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 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
It works! Thank you, Doug.
Ting
On Nov 24, 2014, at 12:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Would mris_decimate work?
On 11/24/2014 01:53 AM, 婷 wrote: Thanks for your reply with detailed explanation. I am interested in what if we apply analysis on native surface first. Still wondering:)
Ting
On Nov 23, 2014, at 8:23 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future.
The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this.
Cheers, Thomas
On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutingxt@gmail.com wrote: Hi Thomas,
I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas?
Thanks,
Ting
On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Ting,
I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister.
Cheers, Thomas
On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutingxt@gmail.com wrote: Dear freesurfer experts,
Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer?
Many thanks,
Ting
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 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
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