Freesurfer / BrainVisa full pipeline

This pipeline performs the following steps:

• Pipeline to import data into a freesurfer database. Please read more information at 01 Create Freesurfer subject from T1 anatomical image process.


• Launch the recon-all freesurfer command line. Please read more information at 02 Launch Freesurfer full pipeline recon-all process.


• Launch the Freesurfer / Brainvisa process to convert to image formats used in BrainVisa (typically, Nifti), to obtain meshes with inter-subjects correspondance, and to use the coordinates system of aims. Please read more information at Freesurfer outputs To BrainVisa conversion pipeline process.

After analysis of many subjects, you can also do:

• 1 Creation of a group of subjects.


• 2 Average brain mesh.


• 3 Average Gyri Texture.

Description

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.

References:

• Tucholka et al. An empirical comparison of surface-based and volume-based group studies in neuroimaging. Neuroimage 2012.


• Roca et al. Inter-subject connectivity-based parcellation of a patch of cerebral cortex. MICCAI 2010.

Parameters

RawT1Image: Raw T1 MRI ( input )

database: OpenChoice ( input )

Technical information

Toolbox : Freesurfer

User level : 0

Identifier : freesurferPipelineComplete

File name : brainvisa/toolboxes/freesurfer/processes/freesurferPipelineComplete.py

Supported file formats :

RawT1Image :

NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image