Dear Freesurfer experts<br><br>I have
encountered a problem of performing fully automated reconstruction of
my T1 image. Attached please find the resulted image after the
reconstruction. The white and pial surfaces do not follow the
boundaries as specified by aseg.mgz segmentation. If I interpret
correctly, the green line should lay on the boundaries between grey and
white matters, and the red line should lay on the boundaries between
CSF and grey matter. But that is not my case. The green and red lines
seem following wrong boundaries, and it affected the later cortical
parcellation stored in aparc+aseg.mgz file. How should I correct or
make edit for my case? Is there anything going wrong in my procedure?<br>

<br>For you information, I just have one T1 volume for each subject, and the version of my installed freesurfer is <span style="color: rgb(51, 51, 255);">4.3.0 </span><br>The command-line I used is <span style="color: rgb(51, 51, 255);">recon-all -i &lt;directory that has the COR files&gt; -s &lt;subject_name&gt; -sd &lt;subjects_dir&gt; -all<br>


<br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">Regards</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">Angel<br><br></span></span>