Hi Ed,

I'm not sure if this'll help you, but I read your question right after I posted mine, and thought to let you know the solution I used in cases where I had to add control points:

" Or Make Life Easier

recon-all -make all -s subjid "

is copied from one of the Freesurfer Powerpoint slides. It worked great for me, and I suspect it will also work in your case. As far as I understand, using this command Freesurfer will look for the first function in the pipeline where some of the input has been modified, and performs all recon-all steps from there.

Cheers,

Jelmer

________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Gronenschild Ed (NP) [ed.gronenschild@maastrichtuniversity.nl] Verzonden: donderdag 25 februari 2016 19:19 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi,

I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments?

Cheers, Ed

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