A question about ribbon-constrained volume to surface mapping algorithm

[xy kong]

Hi everyone, I have a question about volume to surface mapping algorithm.

I checked some subjects' voxel-wise rs-fmri data and his structural surface data in HCP 1200S and found found that there is no voxel in some area of the ribbon, so how did we get the value of the vertex in these area?

As shown in the figure below(/.../100206/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz), the yellow line represents pial and the green represents white.

Any replies would be greatly appreciated!

xiangyu

[Glasser, Matthew]

Is the signal just very low there due to dropout?

Matt.

 

From: xy kong <kongx...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, August 3, 2021 at 12:26 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] A question about ribbon-constrained volume to surface mapping algorithm

 

 

Hi everyone, I have a question about volume to surface mapping algorithm.

 

I checked some subjects' voxel-wise rs-fmri data and his structural surface data in HCP 1200S and found found that there is no voxel in some area of the ribbon, so how did we get the value of the vertex in these area?

 

As shown in the figure below(/.../100206/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz), the yellow line represents pial and the green represents white.

 

Any replies would be greatly appreciated!

 

xiangyu

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[xy kong]

Hi Matt

It is possible that this is the case you mentioned. But is it possible that there is no value in some areas of the ribbon?
Thank you for your reply.

xiangyu

[Glasser, Matthew]

If the FOV of the scan misses part of the brain that could happen.

 

Matt.

 

From: xy kong <kongx...@gmail.com>
Date: Tuesday, August 3, 2021 at 8:27 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matthew" <glas...@wustl.edu>
Subject: Re: [hcp-users] A question about ribbon-constrained volume to surface mapping algorithm

 

 

Hi Matt

 

It is possible that this is the case you mentioned. But is it possible that there is no value in some areas of the ribbon?
Thank you for your reply.

 

xiangyu

在2021年8月3日星期二 UTC+8 下午7:16:34<glas...@wustl.edu> 写道：

Is the signal just very low there due to dropout?

Matt.

 

From: xy kong <kongx...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, August 3, 2021 at 12:26 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] A question about ribbon-constrained volume to surface mapping algorithm

 

 

Hi everyone, I have a question about volume to surface mapping algorithm.

 

I checked some subjects' voxel-wise rs-fmri data and his structural surface data in HCP 1200S and found found that there is no voxel in some area of the ribbon, so how did we get the value of the vertex in these area?

 

As shown in the figure below(/.../100206/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz), the yellow line represents pial and the green represents white.

 

Any replies would be greatly appreciated!

 

xiangyu

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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[Coalson, Timothy Scott (S&T-Student)]

There is also a dilation step (on the surface for cortex), intended more for a different purpose, but if there is an FoV miss, it probably would also dilate values from nearby cortex to fill the hole (though there could easily be a resampling edge effect at the edge of the FoV before the exact zeros that get dilated away).

Tim

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From: Glasser, Matthew <glas...@wustl.edu>
Sent: Tuesday, August 3, 2021 8:29 PM
To: xy kong <kongx...@gmail.com>; HCP-Users <hcp-...@humanconnectome.org>

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/0288CCAD-C546-4E66-99FF-2F24E8976AB9%40wustl.edu.

[xy kong]

Is the dilation you mentioned done in wb_command -volume-to-surface-mapping?

xiangyu

[Coalson, Timothy Scott (S&T-Student)]

No, it is done after that command within the fMRISurface script, looks like this line:

https://github.com/Washington-University/HCPpipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh#L136

When mapping to the native mesh with ribbon mapping, you should dilate a little afterwards anyway, as the tiny vertices from marching cubes often "miss" all voxel subsampling points and don't get assigned a value.

Tim

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From: xy kong <kongx...@gmail.com>
Sent: Thursday, August 5, 2021 1:10 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu>