Hi Anastasia, <div><br></div><div>  I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn&#39;t end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? </div>
<div><br></div><div>  I am going to run bbregister tonight, and I&#39;ll let you know how it goes -- I&#39;m hopeful! </div><div><br></div><div>Thank you again!</div><div><br></div><div>Susie Kuo</div><div>NIH<br><br><div class="gmail_quote">
On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <span dir="ltr">&lt;<a href="mailto:ayendiki@nmr.mgh.harvard.edu" target="_blank">ayendiki@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"><br>
Hi Susie - I&#39;m attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles.<br>


<br>
I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all.<br>
<br>
Hope this helps,<br>
a.y<div><div><br>
<br>
On Tue, 26 Mar 2013, Susan Kuo wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Anastasia,   I did as you recommended and checked the diffusion-to-anatomical<br>
registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be<br>
good. Upon closer inspection, what I find is that there are incipient &#39;bits&#39; of all<br>
the tracts, but they seem to not have &#39;grown&#39;, though they are in the proper space<br>
(comparing them to good brains that yielded the full complement of tracts). Is there a<br>
configuration in your TRACULA that controls the growing of the tracts specifically?<br>
Perhaps I should look into that. <br>
<br>
  Thank you, btw, for your very prompt reply yesterday- it was much appreciated!<br>
<br>
<br>
Sincerely, <br>
Susie Kuo<br>
NIH<br>
<br>
On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki &lt;<a href="mailto:ayendiki@nmr.mgh.harvard.edu" target="_blank">ayendiki@nmr.mgh.harvard.edu</a>&gt;<br>
wrote:<br>
<br>
      Hi Susan - Good to hear that you get good results for most of your<br>
      subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical<br>
      registration for the subjects that are failing? I&#39;d check the<br>
      aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if<br>
      there are any holes or misregistration.<br>
<br>
      a.y<br>
<br>
      On Mon, 25 Mar 2013, Susan Kuo wrote:<br>
<br>
            Hi FreeSurfers and Anastasia,   TRACULA is working great for<br>
            me, generating tracts for a sample of 20 subject<br>
            brains I&#39;m working with. However, for 3 of the brains, I&#39;m<br>
            receiving incomplete and poorly formed tracts.<br>
            I&#39;ve re-run trac-all at least 2x on each subject in case there<br>
            was a mistake in my original configuration.<br>
            However, I am reproducing the same results. Does anybody have<br>
            an idea why I would see these &quot;spotty&quot; tracts? <br>
<br>
<br>
            Thank you for all your help! <br>
<br>
            --<br>
            Susie Kuo<br>
            NIH<br>
<br>
<br>
<br>
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<br>
<br>
--<br>
Susie Kuo<br>
<br>
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. -<br>
Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear<br>
<br>
</blockquote>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div><span style="line-height:19px;color:rgb(69,69,69);font-size:17px;font-family:&#39;Times New Roman&#39;,Times,serif">Susie Kuo</span></div>
<span style="line-height:19px;color:rgb(69,69,69);font-size:17px;font-family:&#39;Times New Roman&#39;,Times,serif"><div><span style="line-height:19px;color:rgb(69,69,69);font-size:17px;font-family:&#39;Times New Roman&#39;,Times,serif"><br>

</span></div>Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,<i> Sherlock Holmes- Valley of Fear</i></span>
</div>