Hi Paola,

you can just run autorecon2-cp. It will run all the steps -wm would, plus a few extra.

cheers, Bruce On Thu, 19 Aug 2010, Paola Valsasina wrote:

Dear FreeSurfer experts,

I am quite new to FreeSurfer and I am trying to analyze some patients. We run -autorecon2 step and we got some errors both in the intensitiy normalization and in the wm segmentation, so what we need to do now is both to add control points to the brainmask.mgz image and to slightly edit wm.mgz to fill holes.

I am reading from the course slides the suggested workflow for running FreeSurfer, and it is suggested that 1) correction of intensitiy is performed (by adding control points and running of -autorecon2-cp) and 2) editing of wm is performed (by editing wm and running -autorecon2-wm). My question is: can I do both these steps together with a command line like:

recon-all -s subject -autorecon2-cp -autorecon2-wm (after having done proper manual edits to both brainmask.mgz and wm.mgz)

Or should I run only

recon-all -s subject -autorecon2-cp, wait for the results of this step, check the wm output and proceed, if necessary, with -autorecon2-wm?

I am asking this basically for saving time, but of course if it is not possible, we are proceeding with two separate steps

Thank you for any advice

Paola

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