Thanks Bruce,<div><br></div><div>So I just need a warp field in .m3z format. Cool. As this distortion correction is proprietary, we don&#39;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.</div><div><br></div><div>Thanks!</div><div>-David</div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Date: Sun, 2 Nov 2014 21:44:23 -0500<br>
From: Bruce Fischl &lt;<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;fischl@nmr.mgh.harvard.edu&#39;)">fischl@nmr.mgh.harvard.edu</a>&gt;<br>
Subject: Re: [Freesurfer] applying manual freesurfer edits to warped<br>
        brain   image<br>
To: Freesurfer support list &lt;<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;freesurfer@nmr.mgh.harvard.edu&#39;)">freesurfer@nmr.mgh.harvard.edu</a>&gt;<br>
Message-ID: &lt;<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;35417931-CE03-4CB8-A30E-C1F34C174B71@nmr.mgh.harvard.edu&#39;)">35417931-CE03-4CB8-A30E-C1F34C174B71@nmr.mgh.harvard.edu</a>&gt;<br>
Content-Type: text/plain; charset=&quot;us-ascii&quot;<br>
<br>
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<br>
<br>
<br>
<br>
&gt; On Nov 2, 2014, at 9:37 PM, David Grayson &lt;<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;dgrayson@ucdavis.edu&#39;)">dgrayson@ucdavis.edu</a>&gt; wrote:<br>
&gt;<br>
&gt; Hi freesurfer experts,<br>
&gt;<br>
&gt; 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?<br>
&gt;<br>
&gt; Thanks in advance for any advice!<br>
&gt;<br>
&gt; -David<br>
&gt; _______________________________________________<br>
&gt; Freesurfer mailing list<br>
&gt; <a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;Freesurfer@nmr.mgh.harvard.edu&#39;)">Freesurfer@nmr.mgh.harvard.edu</a><br>
&gt; <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141102/65628850/attachment-0001.html" target="_blank">http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141102/65628850/attachment-0001.html</a><br>
</blockquote></div>