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PennLINC / qsiprep

Preprocessing of diffusion MRI
http://qsiprep.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Subthalamic nucleus #450

Closed bdeck8317 closed 2 years ago

bdeck8317 commented 2 years ago

Hi @mattcieslak ,

I noticed you had included the parcellation from CIT168 in the construction of some atlases for QSIprep v 16

Does this include the subthalamic nucleus for brainnetome? It wasn't clear based on the following notebook: https://github.com/PennLINC/qsiprep-atlas/blob/main/QSIRecon%20atlases.ipynb.

Furhter, is there a way to include this ROI if it is not included in QSIprep v 16? I have tried to just use mri_concat (fs tool) to concatenate the STN node for each hemi but the resulting dwi connectome (created manually after concatenating to a subject's individual atlas) ignores these two ROIs even when they are appended to the origLUT and mrtrix LUT.

Thanks, Ben

bdeck8317 commented 2 years ago

Closing this issue as you can add these ROIs using freesurfer's mergeseg command and construct a new LUT.