Hi Janessa,
you need to convert your transforms to the MNI .xfm format, then put the transform in the subject's mri/transforms/talairach.xfm file. You should definitely check them with tkregister2 to make sure that there is no offset or other source of conversion-related inaccuracy.
Note though that poor talairch xforms are not the typical cause of poor segmentations. If you send us a sample dataset we'll take a look and see if we can figure out what's going on. Bruce
On Thu, 8 Apr 2010, Jenessa Price wrote:
Hello,
We've noticed that FreeSurfer has been doing a poor job with our data on the first few steps prior to segmentation. All of our data has been aligned and Talairached manually for another project, and we were wondering if it is possible to submit that data into the FreeSurfer pipeline so that it can be segmented from there. If so, what is the command?
Thank you, Jenessa