Hello Bruce,

By creating new errors after adding cp, it usually leaves out a large portion of cortex (and its white matter) that was originally correctly identified in the first attempt. I have tried to add cp in areas that are not in partial volume voxels. The version command says I am using:

$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $

Thanks! Megan

On 8/25/12 8:29 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Megan

it's hard for us to diagnose without seeing the details. In general though you have to be careful to make sure that you aren't putting control points in partial volumed voxels. When you say it creates new errors, can you give us some details? Is the wm too bright in those regions? What FS version are you using?

cheers Bruce

On Fri, 24 Aug 2012, Herting, Megan wrote:

...

Hi,

I have been using freesurfer on a large dataset and I am having some trouble. Sometimes the temporal lobes are not fully covered, so I will go back to add a few control points based on the recommendations of freesurfer (voxels that are <110 and not next to a gray matter voxel) and send it through again. This will often correct the previous error, but then ends up creating new errors in a different region (frontal lobe, temporal lobe in the other hemisphere) etc. This has happened on a large fraction of my data (~25%). What is recommended to fix this? Should I continue to try to add cp to these new regions and send it through again, and continue to do this until it looks good? Is there another method?

Thank you! Megan

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