Hi,
I have some mesh and label files I would like to use with my Freesurfer data however they are in an alternative format (connectome workbench).
I would like to get the labels into the space of a typical Freesurfer subject (e.g. fsaverage), followed by pushing the labels to subject native space and creating volume label files (similar to the aparc native space parcellations).
Is it possible to register an isolated mesh file to the fsaverage subject? How can I convert labels on a .gii mesh file to a standard Freesurfer subject?
Thanks, David
p.s. The goal of this would be to use the following parcellation scheme with my freesurfer data:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.
Hi David
I'm pretty sure that the Wash U HCP group has sorted this out. Have you asked them?
cheers Bruce
On Tue, 8 Mar 2016, Slater David wrote:
Hi,
I have some mesh and label files I would like to use with my Freesurfer data however they are in an alternative format (connectome workbench).
I would like to get the labels into the space of a typical Freesurfer subject (e.g. fsaverage), followed by pushing the labels to subject native space and creating volume label files (similar to the aparc native space parcellations).
Is it possible to register an isolated mesh file to the fsaverage subject? How can I convert labels on a .gii mesh file to a standard Freesurfer subject?
Thanks,
David
p.s. The goal of this would be to use the following parcellation scheme with my freesurfer data:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239–.
Hi Bruce,
I wrote to the HCP user group to ask about this. I received an answer but it’s still unclear to me.
As far as I can tell their are tools which can translate Freesurfer surfaces to the HCP/Caret format, but there isn’t a tool to convert in the opposite direction.
I simply would like to take a surface parcellation in HCP (32k or 164k) format and resample it to a standard Freesurfer subject (e.g fsaverage).
Here is my question and the reply from the HCP user group:
----------------------------------------
Great thanks for your helpful reply.
Unfortunately I'm not working with the HCP data exclusively. In addition we have our own data which has been pre-processed with the standard FreeSurfer -recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, instead they have typical output surfaces from FreeSurfer...
So if I understand correctly I could do the following:
* Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh surfaces for each subject
* The Gordon parcellation would then have a direct correspondence with these meshes (no resampling required)
* The FreeSurfer "mri_label2vol" tool could then be used to create subject specific parcellation maps
Is this correct? Am I missing something?
Thanks,
David
-----Message d'origine-----
De : Donna Dierker [mailto:donna@brainvis.wustl.edu] Envoyé : 08 March 2016 18:05 À : Slater David Objet : Re: [HCP-Users] Cortical parcellations in Connectome Workbench and FreeSurfer
I hope someone who has actually done something like this answers, but this page might be helpful:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol
I'm less familiar with Freesurfer tools, but conceptually:
* The Gordon parcellation is available on 32k mesh (or 164k at least).
* The subject's individual surface is available in both of those meshes.
* The parcellation could be projected to the ribbon between the white and pial surfaces (possibly via mri_label2vol).
* It would not be necessary to resample the parcellation onto the native mesh to do this.
* The subject's native mesh is also available in one of the HCP-downloadable packages.
* There is a way, using -surface-project-unproject, to convert stuff back to native mesh, but it's tough to get your head around it, and I'm not sure it's the shortest path in this case.
Again, hopefully someone who has done this will reply. :)
On Mar 8, 2016, at 4:14 AM, Slater David <David.Slater@chuv.chmailto:David.Slater@chuv.ch> wrote:
Hi,
I have a parcellation I would like to work with from the following paper:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.
The cortical parcellations are saved in .gii format for both the fs_LR 32k and 164k meshes. My aim is to create a parcellated volume image for each of my subjects in their native space. I know how to do this with Freesurfer tools but I am a little lost with the fs_LR 32k and 164k mesh formats.
If I had the parcellation in a standard Freesurfer subject space (e.g. fsaverage) I would transform the parcalletion to the subject native space and convert the surface labels to a volume parcellation. This is similar to how the aparc niftii files are generated.
How can I get a parcellation of the fs_LR 32k or 164k meshes into a subject's native space parcellation? Or alternatively, how can I convert fs_LR 32k or 164k vertex values to the fsaverage surface?
Thanks,
David
-----Message d'origine----- De : freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 08 March 2016 14:32 À : Freesurfer support list Objet : Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels
Hi David
I'm pretty sure that the Wash U HCP group has sorted this out. Have you asked them?
cheers
Bruce
On Tue, 8 Mar 2016, Slater David wrote:
Hi,
I have some mesh and label files I would like to use with my
Freesurfer data however they are in an alternative format (connectome workbench).
I would like to get the labels into the space of a typical Freesurfer
subject (e.g. fsaverage), followed by pushing the labels to subject
native space and creating volume label files (similar to the aparc
native space parcellations).
Is it possible to register an isolated mesh file to the fsaverage subject?
How can I convert labels on a .gii mesh file to a standard Freesurfer
subject?
Thanks,
David
p.s. The goal of this would be to use the following parcellation
scheme with my freesurfer data:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M.,
Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area
Parcellation from Resting-State Correlations. Cereb. Cortex bhu239–.
Hi David
can you explain again what you are trying to do? Hopefully some combination of Matt Glasser or other HCP folks and we can help you.
Bruce
On Thu, 10 Mar 2016, Slater David wrote:
Hi Bruce,
I wrote to the HCP user group to ask about this. I received an answer but it’s still unclear to me.
As far as I can tell their are tools which can translate Freesurfer surfaces to the HCP/Caret format, but there isn’t a tool to convert in the opposite direction.
I simply would like to take a surface parcellation in HCP (32k or 164k) format and resample it to a standard Freesurfer subject (e.g fsaverage).
Here is my question and the reply from the HCP user group:
Great thanks for your helpful reply.
Unfortunately I'm not working with the HCP data exclusively. In addition we have our own data which has been pre-processed with the standard FreeSurfer -recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, instead they have typical output surfaces from FreeSurfer...
So if I understand correctly I could do the following:
- Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh
surfaces for each subject
- The Gordon parcellation would then have a direct correspondence with these
meshes (no resampling required)
- The FreeSurfer "mri_label2vol" tool could then be used to create subject
specific parcellation maps
Is this correct? Am I missing something?
Thanks,
David
-----Message d'origine-----
De : Donna Dierker [mailto:donna@brainvis.wustl.edu] Envoyé : 08 March 2016 18:05 À : Slater David Objet : Re: [HCP-Users] Cortical parcellations in Connectome Workbench and FreeSurfer
I hope someone who has actually done something like this answers, but this page might be helpful:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol
I'm less familiar with Freesurfer tools, but conceptually:
The Gordon parcellation is available on 32k mesh (or 164k at least).
The subject's individual surface is available in both of those meshes.
The parcellation could be projected to the ribbon between the white and
pial surfaces (possibly via mri_label2vol).
- It would not be necessary to resample the parcellation onto the native
mesh to do this.
- The subject's native mesh is also available in one of the HCP-downloadable
packages.
- There is a way, using -surface-project-unproject, to convert stuff back to
native mesh, but it's tough to get your head around it, and I'm not sure it's the shortest path in this case.
Again, hopefully someone who has done this will reply. :)
On Mar 8, 2016, at 4:14 AM, Slater David David.Slater@chuv.ch wrote:
Hi,
I have a parcellation I would like to work with from the following paper:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M.,
Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.
The cortical parcellations are saved in .gii format for both the fs_LR 32k
and 164k meshes. My aim is to create a parcellated volume image for each of my subjects in their native space. I know how to do this with Freesurfer tools but I am a little lost with the fs_LR 32k and 164k mesh formats.
If I had the parcellation in a standard Freesurfer subject space (e.g.
fsaverage) I would transform the parcalletion to the subject native space and convert the surface labels to a volume parcellation. This is similar to how the aparc niftii files are generated.
How can I get a parcellation of the fs_LR 32k or 164k meshes into a
subject's native space parcellation? Or alternatively, how can I convert fs_LR 32k or 164k vertex values to the fsaverage surface?
Thanks,
David
-----Message d'origine----- De : freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 08 March 2016 14:32 À : Freesurfer support list Objet : Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels
Hi David
I'm pretty sure that the Wash U HCP group has sorted this out. Have you asked them?
cheers
Bruce
On Tue, 8 Mar 2016, Slater David wrote:
Hi,
I have some mesh and label files I would like to use with my
Freesurfer data however they are in an alternative format (connectome
workbench).
I would like to get the labels into the space of a typical Freesurfer
subject (e.g. fsaverage), followed by pushing the labels to subject
native space and creating volume label files (similar to the aparc
native space parcellations).
Is it possible to register an isolated mesh file to the fsaverage subject?
How can I convert labels on a .gii mesh file to a standard Freesurfer
subject?
Thanks,
David
p.s. The goal of this would be to use the following parcellation
scheme with my freesurfer data:
Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M.,
Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area
Parcellation from Resting-State Correlations. Cereb. Cortex bhu239–.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Slater David