Estimating fiber endpoints on the cortical surface

[Jason Yeatman]

I have had a few questions about mapping fibers to the cortical surface. I have written a set of routines to do this and they are all within the AFQ 3Dmesh toolbox (AFQ/3Dmesh). This work was first described in the reference below. Start with a freesurfer segmentation. This is essential for defining the gray/white boundary. The function fs_autosegmentToITK will run freesurfer and then make nifti files in a good format. The function AFQ_meshCreate will create an AFQ mesh structure containing the cortical surface as a mesh and useful fields defining various parameters. The function AFQ_meshAddFgEndpoints will map fibers to this cortical mesh. This function is still seeing development and I invite input on better ways to do these computations. It is an interesting and open problem in the field of how to define the cortical endpoints of a fascicle and small changes to the computations can have a large effect. The function AFQ_RenderCorticalSurface will render the cortical mesh and is also a wrapper to run the whole 3Dmesh pipeline. Also see AFQ_meshAddROI for adding a volume ROI to the cortical mesh.

Yeatman J.D., Weiner K.S., Pestilli F., Rokem A., Mezer A., Wandell B.A. (2014). The Vertical Occipital Fasciculus: A Century of Controversy Resolved by In Vivo Measurements. Proc. Natl. Sci. U.S.A

[David Slater]

This looks like a nice idea. I'll try it at some point and let you know what I think.

Thanks for all the tools.

Cheers,
David

[Blue HeronCo]

Hi Jason,

I have been working on creating fiber endpoints on the cortical surface and I have some problems with it. As you recommended, I have completed freesurfer segmentation and created a surface image. To run AFQ_meshCreate I need to have nifti image for the tract endpoint like you have in  ..data/mesh directory (Left_Arcuate_Endpoints.nii.gz).  To create this nifti file for my data, I have run 

dtiFiberendpointNift.m function. To run this I need to have .mat or pbd file for each tract. When I used my fg file as an input, it did not work. Probably, I need to have fg file for each tract separately.  You also have .pbd file for Arcuate and ILF tracts. I am not familiar with this format and could you please help me with creating .pdb file for each tract?

Thanks,

Yildir

[Jason Yeatman]

Yeah you just need to split out one of the individual fiber groups. So, for example fg(19) would be the left arcuate

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[Chris Wertz]

Hi Jason,

I have been generating fiber endpoints and rendering them on the cortical surface. I would like to take the  L_Arcuate_FiberDensity.nii.gz  file as an example and view it on the subject's /surf/lh.inflated image in FreeSurfer. I would like to extract cortical thickness ROIs for each subject depending on where their fiber density endpoints terminate on the cortical surface. I saw that you implemented a registration method " VOF endpoints were projected to the cortical surface and registered to the FreeSurfer group average template" in this paper The vertical occipital fasciculus: A century of controversy resolved by in vivo measurements. Did you use this command to achieve this registration, mri_vol2surf --src L_Arcuate_FiberDensity.nii.gz --out L_Arcuate_FiberDensity.mgh --regheader subject/mri/orig.mgz --hemi lh ?

Thanks,

Chris

[Jason Yeatman]

Yeah something like the command you cited should work. It all depends on the registration of the images. But freesurfer supports visualizing nifti images on the cortical surface. YOu just have to make sure that your diffusion data was aligned to the image that was sent through freesurfer

On Thu, Oct 1, 2020 at 8:48 AM Chris Wertz <cwe...@mrn.org> wrote:

Hi Jason,

I have been generating fiber endpoints and rendering them on the cortical surface. I would like to take the  L_Arcuate_FiberDensity.nii.gz  file as an example and view it on the subject's /surf/lh.inflated image in FreeSurfer. I would like to extract cortical thickness ROIs for each subject depending on where their fiber density endpoints terminate on the cortical surface. I saw that you implemented a registration method " VOF endpoints were projected to the cortical surface and registered to the FreeSurfer group average template" in this paper The vertical occipital fasciculus: A century of controversy resolved by in vivo measurements. Did you use this command to achieve this registration, mri_vol2surf --src L_Arcuate_FiberDensity.nii.gz --out L_Arcuate_FiberDensity.mgh --regheader subject/mri/orig.mgz --hemi lh ?

Thanks,

Chris

On Monday, September 28, 2020 at 11:00:07 AM UTC-6 Jason wrote:

Yeah you just need to split out one of the individual fiber groups. So, for example fg(19) would be the left arcuate

On Sun, Sep 27, 2020 at 3:49 PM Blue HeronCo <bluehero...@gmail.com> wrote:

Hi Jason,

I have been working on creating fiber endpoints on the cortical surface and I have some problems with it. As you recommended, I have completed freesurfer segmentation and created a surface image. To run AFQ_meshCreate I need to have nifti image for the tract endpoint like you have in  ..data/mesh directory (Left_Arcuate_Endpoints.nii.gz).  To create this nifti file for my data, I have run 

dtiFiberendpointNift.m function. To run this I need to have .mat or pbd file for each tract. When I used my fg file as an input, it did not work. Probably, I need to have fg file for each tract separately.  You also have .pbd file for Arcuate and ILF tracts. I am not familiar with this format and could you please help me with creating .pdb file for each tract?

Thanks,

Yildir

On Monday, August 17, 2015 at 3:31:37 PM UTC-7 Jason wrote:

I have had a few questions about mapping fibers to the cortical surface. I have written a set of routines to do this and they are all within the AFQ 3Dmesh toolbox (AFQ/3Dmesh). This work was first described in the reference below. Start with a freesurfer segmentation. This is essential for defining the gray/white boundary. The function fs_autosegmentToITK will run freesurfer and then make nifti files in a good format. The function AFQ_meshCreate will create an AFQ mesh structure containing the cortical surface as a mesh and useful fields defining various parameters. The function AFQ_meshAddFgEndpoints will map fibers to this cortical mesh. This function is still seeing development and I invite input on better ways to do these computations. It is an interesting and open problem in the field of how to define the cortical endpoints of a fascicle and small changes to the computations can have a large effect. The function AFQ_RenderCorticalSurface will render the cortical mesh and is also a wrapper to run the whole 3Dmesh pipeline. Also see AFQ_meshAddROI for adding a volume ROI to the cortical mesh.

Yeatman J.D., Weiner K.S., Pestilli F., Rokem A., Mezer A., Wandell B.A. (2014). The Vertical Occipital Fasciculus: A Century of Controversy Resolved by In Vivo Measurements. Proc. Natl. Sci. U.S.A

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