How to use AAL 90 atlas in Brainstorm?

Discussions
1

Hi Experts,

Thank you all for your great contribution to the community!
I am learning it and surprisingly find it an ideal tool to do neuroscience research.

My question is

I alwasy use freesurfer to reconstruct head model. In freefurser, the Desikan-Killiany atlas and other are used.
In some published papers, some authors said (Low frequency connectivity is associated with mild traumatic brain injury)
“A multi sphere head model was constructed for each individual and brain space was normalized to a standard MNI brain using SPM2”.

“A priori sources (seeds) of interest in the cortex and sub cortical regions were identified from the AAL automated anatomical labeling atlas giving 90 locations for time series to be
extracted and analyzed”
…

If possible, would you like to tell me how to normlize my T1.mgz or brainmask.mgz to MNI, and how to import AAL atlas into scouts tabs?
What I want to do is to extract scouts time series (90 seed points) based on AAL atlas and then to construct a network graph by calculate the correlation between the time series.

Maybe I did not express mine clearly.

In brief, I hope to import AAL atlas into anatomy folder (that is constructed by freesurfer) and calculate correlaton between time courses extracted from AAL atlas.

Best wishes,

Junpeng Zhang

1 Like
2

Hello,

If you want to use this AAL atlas, you have to find a way to have it available on the FreeSurfer surfaces. For this, you have to contact the support for the FreeSurfer software. It looks like this question has been discussed recently (example below) so they might have a solution for you.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27807.html

Normalizing the volumes and processing the sources in volume with SPM2 as your paper suggests is not an optimal approach. If you reconstruct the sources on the cortex, I would recommend you try to do all your analysis on the cortex. Additionally, Brainstorm does not handle full 3D volumes and would not be able to extract the scouts values.
One approach for which exporting to SPM is interesting is for significance testing, but you have to discard most of the time information. See the tutorials “Export source maps to SPM” on the Brainstorm website.

For the details regarding the atlases in FreeSurfer:
http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
You can also try to use BrainSuite:
http://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite

Cheers,
Francois

3

Hi Francois,

Thank you.
I got it and further study it. Once having progress, I will report here.

Cheers,
Junpeng Zhang

4

Hi,

I am also trying to import AAL atlas to Brainstorm, it would be great if you could share how you imported it.

Best and kind regards
Sanjeev

5

The AAL atlas is a volume atlas, not a surface atlas like the others available from the FreeSurfer segmentation folder.

You can import some regions of a volume atlas as scouts, but only for source files that are computed on a volume grid:
http://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource
http://neuroimage.usc.edu/brainstorm/News#Volume_atlases