Hi Julia,<div><br></div><div>After the skull strip was corrected, you should run:</div><div><br></div><div>recon-all -autorecon2 -autorecon3 -s Subject_name</div><div><br></div><div>this will create new surfaces based on new skull strip.</div>
<div><br></div><div>Tanja.<br><br><div class="gmail_quote">On Mon, Aug 22, 2011 at 6:47 AM, Julia Hill <span dir="ltr">&lt;<a href="mailto:julia.hill@neura.edu.au">julia.hill@neura.edu.au</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:Times New Roman;font-size:12pt;color:#000000">Hi Bruce<br><br>I am new to freesurfer and im having a few issues with a number of my scans.  The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas.  When i review the scans afterwards, the pial and WM surfaces haven&#39;t included the original missing sections of the scans.  How do i go back and include these missing sections?<br>
<br>I have attached a screenshots.<br><br>Thank you kindly<br><br>Julia<br><br><br><div><span name="x"></span><div><div><div><div>
	<p style="color:rgb(0, 0, 0);font-family:arial,verdana,helvetica,sans-serif;font-size:12px;font-weight:bold">
		Julia Hill<br>
		Research Assistant</p><p style="color:rgb(0, 0, 0);font-family:arial,verdana,helvetica,sans-serif;font-size:12px;font-weight:bold">School of Psychiatry</p><p style="color:rgb(0, 0, 0);font-family:arial,verdana,helvetica,sans-serif;font-size:12px;font-weight:bold">
University of New South Wales<br>
	</p>
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	<p style="color:rgb(204, 0, 51);font-family:arial,verdana,helvetica,sans-serif;font-size:11px">Previously Prince 
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