Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn&#39;t conform to the 1mm cube isotropic. I am trying to work on it and figure out a solution. However, if I am not, hope its okay to send you the nifti image.<div><br></div><div>Thanks and regards,</div><div><br></div><div>Sampada<br><div><br></div><div><br></div><div><br></div><div>Rnday, March 20, 2016, Bruce Fischl &lt;<a href="mailto:fischl@nmr.mgh.harvard.edu">fischl@nmr.mgh.harvard.edu</a>&gt; wrote:<div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">what do you mean by &quot;adding&quot; an oblique angle? If you mean acquiring the<br>
data obliquely you should be fine as long as the voxels are close to 1mm<br>
isotropic.<br>
<br>
cheers<br>
Bruce<br>
On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:<br>
<br>
&gt; Dear freesurfer experts,<br>
&gt; Does adding an oblique angle during coronal or axial acquisitions of T1w<br>
&gt; images lead to topographical errors during mri_fix_topology process?<br>
&gt;<br>
&gt; Thanks and regards,<br>
&gt;<br>
&gt; Sampada<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt; --<br>
&gt; Sampada Sinha<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
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