What version are you running? The cmd should be -autorecon2-cp -autorecon3
Make sure you put control points in only white matter with no partial volume gm, otherwise things will go very wrong
Cheers
Bruce



On Nov 23, 2012, at 7:01 AM, Catherine Bois <clb542@york.ac.uk> wrote:

ps. could this have anything to do with the script Ive been using during reconstruction? If so, what is the correct command line to use in order to make sure edits to white matter mask/control points and the pial surface are incorporated during reconstruction?

Thanks!

On 23 November 2012 10:06, Catherine Bois <clb542@york.ac.uk> wrote:
Hello,

I have a question re reconstructing brains (ie after doing the edits and running them again to ensure the edits went through). Before the reconstruction, the whole brain was there, however afterwards, large chunks of the brain is missing. Im worried whether this is something to do with the edits i have done; ie can control points/white matter edits actually make parts of the brain "go missing"? Or is it more likely that somewhere along the process the watershed parameters changed/gone wrong? Has anybody else experienced this problem?

Thank you so much for your help

Regards Cathy

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