Using alternative atlas in FreeSurfer parcellation

1

Hi experts out there,

I am preprocessing structural data with FreeSurfer and I wonder if it is possible to use alternative parcellation atlas (e.g., Shen atlas, AAL) other than Desikan-Killiany or Destrieux which are given by default.

I’ve already look at this page https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation, but still stuck since there is no explanation for changing atlas.

If anyone has any idea on this issue, please let us know!
It’ll be a great help :slight_smile:

Thanks!

2

Same question to me. I wonder whether the anatomic subdivision atlas(e.g. AAL) is not commonly used in freesurfer. The atlas in freesurfer seems to be defined by the algorithm and focus on cortex, while AAL is an anatomical segmentation, dividing all the region in brain. Also, the AAL atlas is volumetric and how to convert it into a surf? As I know, the recon-all command is to deal with the brain file, not the atlas.

3

I meet the same question. Do you resolve this issue? @Ward_Jack @racom02

4

You can convert a Volume Atlas to an annot.
mris_seg2annot

With an annot file you train a cortical parcellation atlas in fsaverage space
mris_ca_train → .gcs

With mris_ca_label you transfer the label from fsaverage to the individual brain. → .annot

With mri_aparc2aseg you can generate a Volume file from the individual annot brain. → .mgz

5

Hi all,

I found an amazing tool to implement subject specific parcellation here: faskowit/multiAtlasTT: multi atlas transfer tools for neuroimaging (maTT) (github.com), which was used in a paper titled “Local structure-function relationships in human brain networks across the lifespan” from Nature Communications.

Cheers,
Yunhong

6

Hi cni-md,
Thank you for your suggestions. I encountered difficulties in the first step. mris_seg2annot requires separate input of volume encoded surface segmentation for each hemisphere of the brain, but AAL is whole brain and includes many subcortical regions. How can we obtain the volume encoded surface segmentation file for AAL?
I’d really any help you can provide.
Have a good day !

7

You can project any volume into a surface for that volume. One way is with AFNI’s 3dVol2Surf. The atlas volume and the surface should be in the same space - native, MNI_2009c, MNI_N27, …

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3dVol2Surf_sphx.html