Is subcortical brain involeved in Surface based analysis?

AFNI Message Board
1

Hi
if I am interested in the striatum (subcortical), can i still perform surfaced based analysis?
Thanks.
rujing

2

I don’t think the FreeSurfer surface contains that; not sure about other brain surface-generating programs, either.

–pt

3

As Paul said, the subcortical isn’t included in the surface meshes. The general approach is to do each surface separately (left, right) and then a third analysis for sub-cortical. You could use 3dSurf2Vol to create a mask fo the whole-brain volume that isn’t represented by the surface-based analyses.

-Peter

4

Using IsoSurface, you can generate a simple surface for any region defined either from a segmentation program or by manually drawing with the Draw Dataset plugin. You can map data to the surface using the same 3dVol2Surf as your would for cortical regions. One important issue is the data is not standardized across subjects because there is no common mesh or grayordinate system to make for good nodal correspondence.

5

Hi Peter
Thanks
Did you mean that, for the subcortical, we can only perform the volume-based analyses? And we can use the segmentation (eg. freesurfer) with 3dSurf2Vol to get the subcortical (volume based) analyses.
Is that right? If so, how to get group analyses, as they are not in common space.
rujing

6

Hi Glen
Thanks.
As you said, they are not in common system. If we are interested in the group analyses, any suggestions?
rujing

7

You could subdivide the particular region in which you are interested, and do an ROI analysis for groups of subjects. Here is an example of one way to do that:

https://afni.nimh.nih.gov/afni/community/board/read.php?1,157456,157474#msg-157474

You could nonlinearly align all subjects to a standard template and get a rough correspondence at the surface node level too at a surface from the template or from one of the subjects.

Daniel

8

charujing123 Wrote:

Hi Peter
Thanks
Did you mean that, for the subcortical, we can
only perform the volume-based analyses? And we
can use the segmentation (eg. freesurfer) with
3dSurf2Vol to get the subcortical (volume based)
analyses.
Is that right? If so, how to get group analyses,
as they are not in common space.
rujing

Hi again-

As Daniel said, you can make surfaces. Whether that’s what you really want is an open question. What I’m recommending is what I’ve seen most often published (3 separate analyses). For the volume analysis, you can, as mentioned above, use 3dQwarp to nonlinearly warp your data to a template, then apply that warp to the Freesurfer segmentation for each person and then quantify the activation (e.g. 3dROIstats) of that area for your particular conditions.