Process to interface freesurfer command lines: here you can add a subject into a freesurfer database, also visible in BrainVisa.
Here is the first step to import a new subject into a freesurfer database. This process merely copies one input T1 data, but it avoids command lines and can manage automatically the database in both FreeSurfer and BrainVisa.
Please refer to the description of paramaters below for more information.
In order to launch the recon-all analysis, let's go to the 02 Launch Freesurfer full pipeline recon-all.
RawT1Image: Raw T1 MRI ( entrée )Select a T1 MRI on your disk by using the directory or in a brainvisa database by using the green icon.
subjectName: String ( input ){subject} which corresponds to the following organization in FreeSurfer: {database}/{subjectName}/mri/ori.mgz
database: OpenChoice ( input )Select a freesurfer database. Only database with a freesurfer ontology are available.
AnatImage: RawFreesurferAnat ( sortie )Hidden parameter.
Toolbox : FreeSurfer
Niveau d'utilisateur : 1
Identifiant :
freesurferCreateSubject
Nom de fichier :
brainvisa/toolboxes/freesurfer/processes/Tools/freesurferCreateSubject.py
Supported file formats :
RawT1Image :NIFTI-1 imageAnatImage :FreesurferMGZ