Issue with Converting Yerkes19 to NMTv2.0 with RheMAP

[cghane]

Hi all,

I'm working on transforming data from the Yerkes19 template to the NMTv2.0 space using antsApplyTransforms. As Yerkes19 is a surface-based atlas, I'm attempting to convert it to a volumetric representation using AFNI's 3dSurf2Vol command. However, this process requires a .spec file, which I'm having difficulty generating.

I wanted to confirm if this is the correct approach for converting data from Yerkes19 to NMTv2.0. If not, could you please advise on the recommended procedure?

Thank you in advance for your guidance.

[PRIME-DRE]

If you have the surface data ready in gifti format, workbench commend is handy for converting the data. wb_command -metric-to-volume-mapping Best, Ting From: 'cghane' via NHP-MRI ***@***.***> Date: Wednesday, January 22, 2025 at 13:49 To: PRIME-RE/prime-re.github.io ***@***.***> Cc: Subscribed ***@***.***> Subject: [PRIME-RE/prime-re.github.io] Issue with Converting Yerkes19 to NMTv2.0 with RheMAP (Discussion #88) [EXTERNAL EMAIL] DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe. Hi all, I'm working on transforming data from the Yerkes19 template to the NMTv2.0 space using antsApplyTransforms. As Yerkes19 is a surface-based atlas, I'm attempting to convert it to a volumetric representation using AFNI's 3dSurf2Vol command. However, this process requires a .spec file, which I'm having difficulty generating. I wanted to confirm if this is the correct approach for converting data from Yerkes19 to NMTv2.0. If not, could you please advise on the recommended procedure? Thank you in advance for your guidance. — Reply to this email directly, view it on GitHub<#88>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BBSQQAMUEQQQRN4LJ55VEC32L7RZ7AVCNFSM6AAAAABVVT3HY6VHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZXHA2TQMZVGA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> -- You received this message because you are subscribed to the Google Groups "NHP-MRI" group. To unsubscribe from this group and stop receiving emails from it, send an email to ***@***.******@***.***>. To view this discussion visit https://groups.google.com/d/msgid/nhp-mri/PRIME-RE/prime-re.github.io/repo-discussions/88%40github.com<https://groups.google.com/d/msgid/nhp-mri/PRIME-RE/prime-re.github.io/repo-discussions/88%40github.com?utm_medium=email&utm_source=footer>. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message and any attachments

[afni-dglen]

AFNI's 3dSurf2Vol and @surf_to_vol_spackle do require a spec file, but it's simple to create one for a gifti format file with a command like this:

quickspec -tn GII mysurface1.gii -tn GII mysurface2.gii -spec myspecfile.spec

The @surf_to_vol_spackle command goes a little further than 3dSurf2Vol by filling in holes (empty voxels) that do not get crossed by the line segments connecting the corresponding nodes of the surfaces or by normal vectors.