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.

Add_options: String ( optional, input )

Add option if needed. For instance, sometimes it is necessary to add the -cw256 option if images are larger than 256 voxels. If the freesurfer command fails, the output message can propose to use specific options. To read this kind of information, please refer to the "BrainVISA Show Log" menu (Crtl-L shortcut).

database: Directory ( input )

subject: String ( input )

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

database :

Directory

leftPial :

FreesurferPial

leftWhite :

FreesurferWhite

leftSphereReg :

FreesurferSphereReg

leftThickness :

FreesurferThickness

leftCurv :

FreesurferCurv

leftAvgCurv :

FreesurferAvgCurv

leftCurvPial :

FreesurferCurvPial

leftGyri :

FreesurferParcellation

leftSulciGyri :

FreesurferParcellation

rightPial :

FreesurferPial

rightWhite :

FreesurferWhite

rightSphereReg :

FreesurferSphereReg

rightThickness :

FreesurferThickness

rightCurv :

FreesurferCurv

rightAvgCurv :

FreesurferAvgCurv

rightCurvPial :

FreesurferCurvPial

rightGyri :

FreesurferParcellation

rightSulciGyri :

FreesurferParcellation