On 9/2/13 12:02 PM, "Glasser, Matthew" glasserm@wusm.wustl.edu wrote:

Hi Bruce,

Connectome Workbench commandline utilities can do this with FSL warp fields:

wb_command -surface-apply-warpfield

One needs to use the inverse warp as the <warpfield> argument and the forward warp as the -fnirt <forward-warp>.

Peace,

Matt.

On 9/2/13 11:19 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

A veritable game of telephone! Thanks Jesper. Matt?

On Mon, 2 Sep 2013, Jesper Andersson wrote:

...

Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser.

J

On 2 Sep 2013, at 15:58, Saad Jbabdi saad@FMRIB.OX.AC.UK wrote:

  Hi In Probtrackx, this is done internally.

If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better.

Cheers, Saad

On 2 Sep 2013, at 15:56, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

  you might check on the FSL list. I think I've seen some
  traffic indicating that there are some tools for doing
  this. I'l cc Saad as he might know

  cheers
  Bruce


  On Mon, 2 Sep 2013, Douglas Greve wrote:

        Hi Shani, I don't think you can apply a FNIRT
        transform to a surface.
        doug
        On 9/2/13 8:20 AM, Shani Ben Amitay wrote:
             Dear freesurfer people,
        Any idea whether I can apply transformation
        that was calculated by fsl
        fnirt on the white/pial surfaces calculated
        using the freesurfer
        stream?
        Thanks!
        Shani
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