Creating AAL .dlabel. file

[Iván Mindlin]

Hello, 

I am having a very hard trouble understanding wb_command documentation.

I want to create a .dlabel file that contains 90 regiones form AAL (cortical and subcortical)

I understand that I should create a label volume for cortical and another for subcortical following the format described in -volume-label-import . Then I should pass these to the -cifti-create-label command using the -volume option .

I need to do this separately for each hemisphere. When I observe the generated "label volume" it did not seem to do any extraction of the relevant parcels. I don't understand which steps are missing nor where to look for any examples

Thanks in advance

[Glasser, Matt]

There is quite a bit of literature recommending against using AAL as a functionally relevant brain parcellation.  Here is a parcellation appropriate for the HCP:

 

https://balsa.wustl.edu/file/87B9N

 

Matt.

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[Iván Mindlin]

Hi Matt, 

Thank you for answering. You are right about that, but the coordinators of the project did not follow my advice

I need the AAL90 in CIFTI format to pass it to a brainsmash function

I expected -volume-label-import to give me the selected parcels and on top of that I do not understand what the structure-label-volume should be.

If anyone can help me understand these concepts I would really appreciate it

Best, 

Ivan

[Tim Coalson]

Cifti generally expects the cortical data to be in surface format (.func.gii, .label.gii), not volume format (see wb_command -cifti-help).  Mapping volume data to the surface is valid within a single individual, but problematic for group-representative data, because volume alignment doesn't manage to align human cortical folding patterns in most of the brain, as we show in our paper:

 https://www.pnas.org/doi/full/10.1073/pnas.1801582115

So, at the very least, you would need a freesurfer run on the anatomical image AAL is based on, if you need to continue down this suboptimal, higher-effort path.  The structure-label-volume file Should generally be the Atlas_ROIs file in here:

https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates

A simpler way is to use -cifti-create-dense-from-template with the dscalar file in that folder as the template.  The HCP MMP 1.0 is already in cifti format, presumably ready for use in brainsmash.

Tim

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