I have had a similar problem with control points where they sometimes don't make any difference on the second time through, even when I use a bunch of them.

Richard Bantz wrote:

freesurfer,

Control points seem to work for some scans and not others. The 

enclosed pictures illustrate a case in which cp's are added to wm but when re-run the wm does not take( 12 slices ). I have tried this twice and both times the same results, is there a fix?

                 Thankyou,
            Richard M Bantz

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

hard to tell from a single slice, but it looks like the skull stripping removed a bunch of the lh temporal lobe, so the control points can't recover it. You need to correct the watershed first.

cheers, Bruce On Mon, 20 Nov 2006, Richard Bantz wrote:

freesurfer,

Control points seem to work for some scans and not others. The

enclosed pictures illustrate a case in which cp's are added to wm but when re-run the wm does not take( 12 slices ). I have tried this twice and both times the same results, is there a fix?

                 Thankyou,
            Richard M Bantz