Hi Ron, we do use the talairach for things like estimating icv, so that would concern me a bit. I don't think there is a straightforward way to insert the skull stripped image into our stream though. Maybe Nick has a better idea?
Bruce On Thu, 28 Jan 2010, Pierson, Ronald K wrote: > We have a large number of scans with excellent, visually inspected and > manually trimmed brain masks, so we would like to use these masks to > assist the FreeSurfer processing. One way we have experimented with to > achieve this is to clip the T1 to remove anything non-brain before > importing it into the subject directory. In using brain-clipped T1 > images as a starting point for FreeSurfer we notice that the Talairach > transform checking is quite far off, scaled badly and rotated downward > 10+ degrees in pitch. I assume that this is due to the lack of > similarity to the moving image, which includes skull. However, even if > we don't modify this transform, the final parcellation looks quite good, > and very, very similar to that from using a standard, non-clipped T1 as > input. Is there any reason not to use a clipped T1 as input into > FreeSurfer? Is the Talairach-based information used for segmentation or > parcellation, and are we potentially creating problems? Or would it be > better to simply use our mask to trim up the images after autorecon1 > (coregistering them into the same image space and clipping them with a > custom routine)? > > > > Ron Pierson > > > > Department of Psychiatry > > Carver College of Medicine > > W-278 GH, 200 Hawkins Dr > > Iowa City, IA 52242 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
