Thanks Bruce,

So I just need a warp field in .m3z format. Cool. As this distortion correction is proprietary, we don't actually get the warp fields, which is silly. But I was thinking since scanner distortions are subtle and coarse, it should be sufficient to nonlinearly register the two unsegmented images using a simple intensity-based volumetric registration at a coarse warp resolution. Would the mri_cvs_register tool be suitable for this if I supply the --step3 flag? Otherwise I am stuck with trying to go between Freesurfer and another set of tools.

Thanks! -David

Date: Sun, 2 Nov 2014 21:44:23 -0500

From: Bruce Fischl <fischl@nmr.mgh.harvard.edu javascript:;> Subject: Re: [Freesurfer] applying manual freesurfer edits to warped brain image To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu javascript:;

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Message-ID: <35417931-CE03-4CB8-A30E-C1F34C174B71@nmr.mgh.harvard.edu javascript:;> Content-Type: text/plain; charset="us-ascii"

What format is the distortion field stored in? If you can get it into .m3z I believe we have tools to do what you want

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On Nov 2, 2014, at 9:37 PM, David Grayson <dgrayson@ucdavis.edu

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Hi freesurfer experts,

I have two T1 images from the same subject acquired at the same time

point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. What I would like now is to have the freesurfer segmentations on the uncorrected image and preserve as much as possible the manual edits. In other words, I would like to warp the surface meshes already obtained on the distortion corrected image to the uncorrected image. Is there already a suggested method that is optimal for this purpose?

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Thanks in advance for any advice!

-David _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer