02 Launch Freesurfer full pipeline recon-all

Process to interface freesurfer command lines: here you launch the recon-all command with or without option just by selecting the subject with the AnatImage parameter.

Parameters

AnatImage: RawFreesurferAnat ( input )
Select a T1 MRI.
database: Directory ( input )
subject: String ( input )
force_fov_to_256: Boolean ( input )
qcache_for_group_analysis: Boolean ( input )
add_other_options: String ( optional, input )
nu: Nu FreesurferAnat ( output )
ribbon: Ribbon Freesurfer ( output )
leftPial: BaseFreesurferType ( output )
Hidden parameter.
leftWhite: BaseFreesurferType ( output )
Hidden parameter.
leftSphereReg: BaseFreesurferType ( output )
Hidden parameter.
leftThickness: BaseFreesurferType ( output )
Hidden parameter.
leftCurv: BaseFreesurferType ( output )
Hidden parameter.
leftAvgCurv: BaseFreesurferType ( output )
Hidden parameter.
leftCurvPial: BaseFreesurferType ( output )
Hidden parameter.
leftGyri: FreesurferGyriTexture ( output )
Hidden parameter.
leftSulciGyri: FreesurferSulciGyriTexture ( output )
Hidden parameter.
rightPial: BaseFreesurferType ( output )
Hidden parameter.
rightWhite: BaseFreesurferType ( output )
Hidden parameter.
rightSphereReg: BaseFreesurferType ( output )
Hidden parameter.
rightThickness: BaseFreesurferType ( output )
Hidden parameter.
rightCurv: BaseFreesurferType ( output )
Hidden parameter.
rightAvgCurv: BaseFreesurferType ( output )
Hidden parameter.
rightCurvPial: BaseFreesurferType ( output )
Hidden parameter.
rightGyri: FreesurferGyriTexture ( output )
Hidden parameter.
rightSulciGyri: FreesurferSulciGyriTexture ( output )
Hidden parameter.

Technical information

Toolbox : Freesurfer

User level : 1

Identifier : freesurferPipeline

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

Supported file formats :

AnatImage :
FreesurferMGZ, FreesurferMGZ
database :
Directory, Directory
nu :
FreesurferMGZ, FreesurferMGZ
ribbon :
FreesurferMGZ, FreesurferMGZ
leftPial :
FreesurferPial, FreesurferPial
leftWhite :
FreesurferWhite, FreesurferWhite
leftSphereReg :
FreesurferSphereReg, FreesurferSphereReg
leftThickness :
FreesurferThickness, FreesurferThickness
leftCurv :
FreesurferCurv, FreesurferCurv
leftAvgCurv :
FreesurferAvgCurv, FreesurferAvgCurv
leftCurvPial :
FreesurferCurvPial, FreesurferCurvPial
leftGyri :
FreesurferParcellation, FreesurferParcellation
leftSulciGyri :
FreesurferParcellation, FreesurferParcellation
rightPial :
FreesurferPial, FreesurferPial
rightWhite :
FreesurferWhite, FreesurferWhite
rightSphereReg :
FreesurferSphereReg, FreesurferSphereReg
rightThickness :
FreesurferThickness, FreesurferThickness
rightCurv :
FreesurferCurv, FreesurferCurv
rightAvgCurv :
FreesurferAvgCurv, FreesurferAvgCurv
rightCurvPial :
FreesurferCurvPial, FreesurferCurvPial
rightGyri :
FreesurferParcellation, FreesurferParcellation
rightSulciGyri :
FreesurferParcellation, FreesurferParcellation