Hi Bruce,

So technically speaking I guess I have three different brain atlases for neonates, 1 yr olds, and 2 yr olds. Each atlas contains a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. I obtained these from a study done by UNC ( http://bric.unc.edu/ideagroup/free-softwares/unc-infant-0-1-2-atlases/ http://bric.unc.edu/ideagroup/free-softwares/unc-infant-0-1-2-atlases/ ).

I also have about 40 different infant fMRI's that I would like to reconstruct and analyze with FreeSurfer. However, I believe that the default template (average.curvature.filled.buckner40.tif) will not work for these infant brains. My end goal is to be able to convert the provided brain atlases (from UNC) into a format that can be used for a template in FreeSurfer (i.e. TIFF image).

Is there any clear cut way to do that?

Thanks for the help.

- Mark

On Mon, Jun 24, 2013 at 3:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Mark

can you clarify what you mean? What template are you referring to?

Bruec

On Mon, 24 Jun 2013, Mark Plantz wrote:

Hello freesurfers,

...

  I am currently attempting to create my own .tiff templates for a

series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have the templates in .nii.gz, .mgz, and .img/.hdr formats.

Is there any easy way to convert from one of these formats to a .tiff image to use as an actual template for reconstruction with FreeSurfer?

If so, would the conversion distort/ruin the template?

Thank you!

• Mark Plantz

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