Hello.<div><br></div><div>I&#39;m a new Freesurfer question, and I was wondering if you could answer a couple of questions for me.  </div><div><br></div><div>First some background:  After having done the autorecon1 and autorecon2 steps successfully, and after also checking and making sure that the original white matter surface registered well to Talairach space, I am now at the point of checking the white matter surface.  There are definitely places that should be included as white matter that were left out.  In those spots, I have added control points and have had no trouble.  </div>


<div><br></div><div>My questions though are about spots in the cortex where the white matter surface has included gray matter.  I believe I should use the Edit Voxels Tool to fix this, but I am not entirely sure how I should &quot;Configure the Brush Info&quot; or &quot;Configure the Volume Brush&quot;.  For the Brush Info, should I set the Target as the Main Volume, the Aux Volume or the Main and Aux Volume?  I am not sure which I should select.  From the tutorial (<a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits" target="_blank">http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits</a>), it looks like I should select the Aux Volume and then save that in order to run: </div>


<div><span style="font-family:courier, monospace;font-size:16px;white-space:pre-wrap">recon-all -autorecon2-wm -autorecon3 -subjid wm2_edits_before.</span></div><div><br></div><div><span style="font-family:courier, monospace;font-size:16px;white-space:pre-wrap"><span style="font-family:arial;font-size:small;white-space:normal">But, I&#39;m concerned about what the tutorial means as the deletion of voxels by this editing tool.  Would reclassifying these voxels as non-white matter automatically render them as part of the pial surface when the above script is run?  Or, would they be reclassified as non-brain tissue?</span></span></div>

<div><br></div><div>Also, I would appreciate it if you could direct me on how to set the Volume Brush Info appropriately.</div><div><br></div><div>Thank you in advance for your help,<br>Meghana</div><div><br></div><div><br>

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<div><br clear="all"><br>-- <br>Meghana Karnik-Henry, Ph.D.<br>Research Associate<br>University of Texas at Dallas<br>Center for Brain Health<br>Department of Behavioral and Brain Sciences<br>
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