01 Create Freesurfer subject from T1 anatomical image

Process to interface freesurfer command lines: here you can add a subject into a freesurfer database, also visible in BrainVisa.

Description

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.

Parameters

RawT1Image: Raw T1 MRI ( input )

Select a T1 MRI on your disk by using the directory or in a brainvisa database by using the green icon.

time_point: OpenChoice ( input )

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 ( output )

Hidden parameter.

Technical information

Toolbox : Freesurfer

User level : 1

Identifier : freesurferCreateSubject

File name : brainvisa/toolboxes/freesurfer/processes/Tools/freesurferCreateSubject.py

Supported file formats :

RawT1Image :

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

AnatImage :

FreesurferMGZ, FreesurferMGZ