How to Map Grayordinates Space Coordinates to MNI Space Coordinates

[李佳艺]

Dear All,

I hope this email finds you well. I would like to identify suitable targets for neuromodulation of working memory based on group-level average activation maps of the S1200 data. Yet, when I examined the CIFTI file, I found the vertex locations for the surface representation are not provided, and some regions are not assigned in the MNI space atlas.

I was wondering if there is a way to map between the grayordinates space and MNI space to obtain the corresponding coordinates of these regions in the MNI space. Any insights or recommendations on how to address this issue would be greatly appreciated.

Thank you in advance for your help!

Best regards,
Jiayi Li

[Tim Coalson]

Vertex coordinates are in .surf.gii files, but they are specific to each individual, and the group averages of these coordinates are not great as representations of the location/folding in a typical subject, even with nonlinear volume registration.

Fundamentally, volume registration does not have good alignment of many parts of the cortex in humans, largely because the folding patterns have a lot of individual variations that would require absurd distortions to "flatten and re-fold" to match other subjects.  Surface-based methods get around this problem by establishing cross-subject correspondence without anatomical deformation fields.  Areal feature registration and the cifti file format improve on this by aligning based on features that identify functional areas and combining the surface data with subcortical structures into a single file for easier full-brain data handling.  See our paper for details about the improvements over volume-based analysis:

https://www.pnas.org/doi/abs/10.1073/pnas.1801582115

However, as a result of surface methods largely ignoring anatomical coordinates when establishing correspondence, the group average surfaces are smoother than individual surfaces, particularly in areas of high folding variability, and as such are mostly only useful for display or approximation.  You should instead use the MMP areas with each individual's surface files (.surf.gii), usually midthickness, to find where in the volume that piece of cortex is in that subject.  In essence, for the cortex, every human subject has its own version of MNI space that is substantially more accurate to that subject's data than any groupwise version of MNI space.

For TMS or other spatially-targeted interventions, it would make more sense to work in the subject's rigid-aligned space (the T1w/ folder in our data), rather than one that has been distorted to look more like the MNI template.  However, I understand there are some assumptions built into some software used for this - if we knew the details of how the software translates between MNI and subject space, in theory you could calculate where the target should be in subject space accurately, and then put it through the reverse transform before giving it to the software, to achieve the correct positioning.

On the other hand, TMS has a pretty large effect zone as I understand it, so "ballpark coordinates" may usually hit the area of interest anyway.

Tim

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[Glasser, Matthew]

Some literature suggests that targeting TMS to individual cortical areas is a good idea.

Matt.

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[李佳艺]

Dear Tim and all
Thank you so much! Your answer has been a great help to me. The individual's vertex coordinates are exactly what I needed. After receiving your email, I tried to obtain the vertex coordinates I was looking for by aligning the 32,492 x 3 vertex coordinates stored in the individual's cortex_left.MSMALL.32k_fs_LR.surf.gii with the 32,942 x 1 sequence in the cortex_left of Q1-Q6.dlabel.nii. I'm unsure if this method of obtaining individual vertex coordinates is correct. While, I noticed that the sequence of coordinates stored in MSMALL.32k_fs_LR.surf.gii differs between individuals, Yet, when viewed in Connectome Workbench, they appear to be the same, which is puzzling to me. 

Additionally, I understand that MSMALL.32k_fs_LR.surf.gii represents a mesh in MNI space, meaning the coordinates stored within are spatial informatio in MNI space. Is there a command that can help convert MSMALL.32k_fs_LR.surf.gii from MNI space to native space?.

Thank you for your guidance and assistance.

Best regards,

Jiayi Li

[李佳艺]

Hi Matt,

Yes, this is exactly the research I'm interested in! I'm so happy to have learned the method for obtaining individual vertex coordinates. Thank you for the guidance. Wishing you a wonderful day.

Best regards,

Jiayi Li

[Tim Coalson]

The coordinates are different per subject because the subjects' cortical folding patterns are different, so the same functional-specific piece of cortex is at different coordinates, even with nonlinear volume alignment.  The surface files in each subject's folder are derived from the segmentation of their anatomical images.

We provide two versions of many of the individual surfaces, in this case T1w/fsaverage_LR32k/*.surf.gii, and MNINonLinear/fsaverage_LR32k/*.surf.gii .  The files under T1w/ use rigidly-aligned coordinates.  While you will need to handle any disagreement between this rigidly-aligned space and your neuromodulation alignment space, it has only rotation and translation compared to that individual's actual head (no scaling, shear, or nonlinear changes, only corrections for known scanner distortions).

The MSMAll surfaces are appropriate for the HCP MMP dlabel file (either MNINonLinear/ or T1w/, depending on what coordinate system you want).

Tim

[李佳艺]

Hi, Tim

I found the MSMALL.surf.gii file I needed in the T1w/fsaverage_LR32k  folder. Thank you for your help. Wishing you a wonderful day.

Best regards,

Jiayi Li