Freesurfer / BrainVisa full pipeline

This pipeline performs the following steps: After analysis of many subjects, you can also do:


One of interests in BrainVISA use is the ability to interface many software dedicated in neuroimaging (actually, BrainVISA can be extended in many ways). In this pipeline, an interface is proposed from very interesting analysis available in Freesurfer (grey/white matter segmentation, cortical parcellation, cortical thickness...) to the BrainVISA environment (database manager, aims coordinate system, visualization in Anatomist...).

Thanks to this pipeline, the following freesurfer outputs can be used in the BrainVISA environment (aims coordinate system): ?h.pial, ?h.white, ?h.sphere.reg, ?h.aparc.annot, ?h.aparc.a2009s.annot, ?h.avg_curv, ?h.curv, ?h.curv.pial ?h.thickness. Furthermore, a normalization of the number of nodes and their indexation is performed in order to compare meshes nodes by nodes across subjects.

By using these processes, the organization of freesurfer database is automatically taken into account and it is completed with new brainvisa outputs.



RawT1Image: Raw T1 MRI ( input )
database: Choice ( input )

Technical information

Toolbox : Freesurfer

User level : 0

Identifier : freesurferPipelineComplete

File name : brainvisa/toolboxes/freesurfer/processes/

Supported file formats :

RawT1Image :
NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image