Hi Bruce,<div><br></div><div>Thank you very much for taking a look at this for us.  I uploaded it to your ftp server under the name JeffSadino_050089_S05.tar.  About 70 of our subjects are showing similar problems.  It seems to be happening more frequently in fs5 as compared to fs4.  If you can find anything that will help, that would be great.  Thank you again!</div>

<div><br></div><div>Jeff<br><br><div class="gmail_quote">On Wed, Oct 5, 2011 at 2:41 PM, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu">fischl@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;">

<div bgcolor="#FFFFFF"><div>Hi jeff</div><div>Sorry, this slipped through the cracks. If you upload the dataset we will take a look</div><div>Bruce</div><div><div></div><div class="h5"><div><br><br></div><div><br>On Oct 5, 2011, at 8:32 PM, Jeff Sadino &lt;<a href="mailto:jsadino.queens@gmail.com" target="_blank">jsadino.queens@gmail.com</a>&gt; wrote:<br>

<br></div><div></div><blockquote type="cite"><div>Hello FreeSurfer Experts,<div><br></div><div>Does anyone have any ideas about how to salvage this data?</div><div><br></div><div>Thank you very much!</div><div>Jeff<br><br>

<div class="gmail_quote">On Sun, Oct 2, 2011 at 5:10 PM, Jeff Sadino <span dir="ltr">&lt;<a href="mailto:jsadino.queens@gmail.com" target="_blank"></a><a href="mailto:jsadino.queens@gmail.com" target="_blank">jsadino.queens@gmail.com</a>&gt;</span> wrote:<br>



<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi Freesurfer Team,</div><div>When we tried to process some subjects in FS 5.0.0 through the cross-sectional step in the longitudinal processing stream, we got inaccurate surfaces generated.  Also, after doing skullstripping or adding control points and re-running the cross-sectional reconstruction, inaccurate pial and white matter surfaces were generated (see attached pictures).  We are not sure how to fix this problem and this has affected about 70 of our scans.  Several of these subjects we also processed in FS 3 and FS 4.3.1, and the surfaces were generated fine.  Are there any known solutions to fixing the surfaces in the newer FreeSurfer?  If not, then could we feed the 4.3.1 cross-sectionals into FS 5 to create the base template, and then use FS 5 to create the longitudinal reconstructions?</div>





<div><br></div><div>Thank you,</div><div>Jeff Sadino</div><font color="#888888"><div><br></div>
</font></blockquote></div><br></div>
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