You can try using bbregister. Normally, you don't use bbregister on a segmentation, but the segmentation index numbers just happen to be "T1-weighted".
doug
ps. Please remember to copy the list when responding. thanks!


On 7/23/13 9:51 AM, Mark Plantz wrote:
Hi Doug,

   Sorry about that vague explanation. So I received a series of infant brain atlases from a UNC medical research group (http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases). I have a series of infant MRI's that I would like to segment (using the infant atlases, instead of the default adult atlas in FreeSurfer). 

   As a preliminary step, I was attempting to check the alignment of one of the atlas files ('avgseg.mgz') with one of the input brains ('brain.mgz'). [I attached these two files, just in case].

So my command line would be:

tkmedit $Subject brain.mgz -segmentation avgseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

The result was the previously attached image. I was just wondering if there is any way to shift the two images manually so the alignment is better? Or maybe the two files are simply not compatible with one another?

Thanks for all the help!

Best,

Mark 




On Mon, Jul 22, 2013 at 3:53 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Mark, I have no idea what you are doing. Can you send a command line?
Are either of the images generated by FS?
doug




On 07/22/2013 03:56 PM, Mark Plantz wrote:
> Hello FreeSurfers,
>
>     I recently obtained a set of infant templates. Out of curiousity,
> I decided to view one of the input brains with the provided segmented
> volume file. It appears that there is some misalignment. I wouldn't
> expect the alignment to be perfect, since I am basically overlaying an
> average of multiple brains onto one. However, it looks like this
> misalignment may be caused by either: 1.) the segmentation volume file
> being shifted down or 2.) the slices not lining up properly (i.e. one
> file starts before the other).
>
>    Any ideas what could cause a problem like this? Could it be that
> the segmented files are simply not compatible with FreeSurfer?
>
> Thanks for the help,
>
> Mark
>
>
>
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