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aramis-lab / clinica

Software platform for clinical neuroimaging studies
http://www.clinica.run/
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DWI connectome question #343

Closed asd567 closed 3 years ago

asd567 commented 3 years ago

Pipeline Which Clinica's Pipeline is concerned ? clinica run dwi-connectome CAPS

From the outputs it seems used the t1-freesurfer's result (/mri/aparc.a2009s+aseg.nii.gz) , and I want to know that if clinica can use AAL2 ?

alexandreroutier commented 3 years ago

Hi @asd567,

Thanks for your interest in Clinica. Currently, dwi-connectome handle only Destrieux and Desikan atlas. This is due to the fact that these atlases are cortical parcellations (explained in FreeSurfer wiki whereas AAL2, AICHA & cie are volume atlases.

As a result, you would need to convert the (volume-based) AAL2 atlas into an atlas compatible with FreeSurfer. Then, apply this parcellation to your data. Finally, dwi-connectome would need some modifications (see https://github.com/aramis-lab/clinica/blob/dev/clinica/pipelines/dwi_connectome/dwi_connectome_utils.py for modifications to performed) before having connectivity matrices for AAL2.

Best, Alex