Gyrification and Sirface area HCP-Young Adults

[Matteo Kostner]

I am a Master’s student currently working on my thesis.                I am developing a pipeline to extract cortical metrics from the HCP-Young Adult dataset, and I would appreciate your guidance to ensure my methodology for calculating gyrification and surface area is technically sound.

 My proposed steps are:

1. Gyrification: I calculate the pial_lgi (local gyrification index) in FreeSurfer. I then convert this to a GIFTI file using the white-matter surface geometry as a reference.              a)  recon all -s < subject> -localGI                b) mris_convert -c pial_lgi white pial_lgi.shape.gii            c) wb_command -metric-resample \ pial_lgi.shape.gii \ sphere.reg.reg_LR.native.surf.gii \ sphere.32k_fs_LR.surf.gii \ BARYCENTRIC \ /rh.pial_lgi.32k_fs_LR.shape.gii

2. Surface Area: I take the lh.area and rh.area files from the FreeSurfer outputs, convert them to GIFTI format, and resample them into the 32k_fs_LR surface space.                        a) mris_convert -c lh/rh.area lh/rh.white lh/rh.area.surf.gii b) wb_command -metric-resample \ lh/rh.area.surf.gii \ subj.R.sphere.reg.reg_LR.native.surf.gii \ subj.L/R.sphere.32k_fs_LR.surf.gii \ BARYCENTRIC \ lh/rh.area.32k.shape.gii

I want to ensure that my resampling steps, particularly the use of white-matter geometry as a reference for the LGI conversion, maintain the integrity of the data across the 32k mesh.

Are there specific flags in wb_command or nuances in the HCP-specific registration that I should be accounting for to ensure these metrics are correctly aligned with the standard 32k_fs_LR templates?

I want to learn from your expertise and would be very grateful for any corrections or suggestions you might have. 

Best regards,

[Glasser, Matthew]

For surface vertex areas you need to compute it from the midthickness and on the mesh you want to use it on, not resample it.  We provide midthickness surface area files here:

 

GIFTI:

${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness_MSMAll_va.32k_fs_LR.shape.gii

${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness_MSMAll_va.32k_fs_LR.shape.gii

 

CIFTI:

${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.midthickness_MSMAll_va.32k_fs_LR.dscalar.nii

 

Hopefully Nagehan and Tim can help with the local gyrification index, which I don’t personally use.

Matt.

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[Matteo Kostner]

Thank you very much Dr. Glasser !  

So to calculate the surface area i should: 

 #  Left hemisphere
wb_command -surface-vertex-areas \

    ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness_MSMAll_va.32k_fs_LR.shape.gii \

    ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/{Subject}.L.vertex_areas.shape.gii

#  Right hemisphere
wb_command -surface-vertex-areas \
    ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness_MSMAll_va.32k_fs_LR.shape.gii \
    ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/{Subject}.R.vertex_areas.shape.gii

[Glasser, Matthew]

They are already computed in the HCP-YA data, but that is how it was done.  We always identify the surface registration if it is not the default MSMSulc in our file names.

[Tim Coalson]

To clarify, the input to -surface-vertex-areas would need to be a surface geometry file (.surf.gii), not a .shape.gii .  The "_va" files are already the vertex areas.

Gyrification index is fine to resample, but the "reg.reg_LR" spheres are not the recommended registration (uses the freesurfer registration, which has strong distortion, and an older atlas registration between freesurfer and fs_LR).  Depending on what your hypothesis is, we recommend either the MSMSulc (folding, gentle) or MSMAll (functional, myelin, etc) registered spheres instead.

Tim

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