Hi Gabriel, -autorecon-pial is equivalent to -autorecon2-pial, although in 5.2 there are some additional stats steps, but basically the same.

You can always look at the flag definitions in the recon-all script to see what exact steps a certain flag triggers.

emacs $FREESURFER_HOME/bin/recon-all

-Louis

5.1: DoSmooth2 DoInflate2 DoSegStats DoCurvStats DoSphere DoSurfReg DoContraSurfReg DoAvgCurv DoJacobianWhite DoCortParc DoPialSurfs DoParcStats DoCortParc2 DoParcStats2

5.2: DoSmooth2 DoInflate2 DoSegStats DoCurvStats DoSphere DoSurfReg DoContraSurfReg DoAvgCurv DoJacobianWhite DoCortParc DoPialSurfs DoPctSurfCon DoParcStats DoCortParc2 DoParcStats2 DoCortParc3 DoParcStats3 DoCortRibbonVolMask DoAParc2ASeg DoWMParc DoBaLabels DoLabelExvivoEC

On Thu, 25 Apr 2013, obregon@nmr.mgh.harvard.edu wrote:

Hi,

I was wondering if the -autorecon2-pial flag has been superseded on the newer release of Freesurfer, for it isn't being recognized?

Also, is the use of this flag equivalent to running recon-all with the -autorecon-pial option?

Thanks,

Gabriel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer