I think the resolution is important. The CA1 subfield is only about 2-2.5 mm thick after all. <br><br>If this is a feature request thread now, let me add that it would be nice if the actual training algorithm was integrated into Freesurfer. There is a lot of disagreement about the most appropriate subfield boundaries, and the ability to make custom training sets would be helpful.<br>

<br>Right now there is little guidance on what kind of data-sets are appropriate to use with this algorithm. I am concerned that users are trying to segment subfields with older data-sets that probably aren&#39;t appropriate (e.g. 1.5 Tesla or 1.5 mm isotropic data). <br>

<br><br><div><div><font color="#999999">Josh</font><font color="#999999"></font></div></div>
<br><br><div class="gmail_quote">On Tue, May 28, 2013 at 1:44 PM, Juan Eugenio Iglesias <span dir="ltr">&lt;<a href="mailto:iglesias@nmr.mgh.harvard.edu" target="_blank">iglesias@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Josh,<br>
as of now, it uses nu.mgz, which is conformed and bias field corrected<br>
with N3.<br>
Koen, do you think we should add a flag to change this? The algorithm is<br>
pretty resolution-independent, and could certainly benefit from<br>
higher-res data.<br>
Cheers,<br>
/Eugenio<br>
<div><div class="h5"><br>
On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:<br>
&gt; I have read that the hippo-subfield algorithm uses the aseg for<br>
&gt; initialization, and then uses the original MRI data. By original, does<br>
&gt; that mean it up-samples the conformed 1mm data to .5mm, or does that<br>
&gt; mean it takes the original original input (i.e. my 0.7 mm isotropic<br>
&gt; MPRAGE) and upsamples it to .5mm?<br>
&gt;<br>
&gt; Josh<br>
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Juan Eugenio Iglesias, PhD<br>
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