Hi Jake

there are voxels like 173, 112, 122 that are incorrectly segmented as wm (that is, they have a value >=5 in the wm.mgz) that connect two adjenct gyri. You can either change the intensity thresholds in mri_segment, or manually erase some of them. The best way to see this is to look at the surface prior to topology correction, and color it with defect numbers so you can see where the defects are. Something like:

cd $SUBJECTS_DIR/<subject id>/mri
freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \
        -f ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1,255:edgecolor=overlay \
        -slice 172 123 134


if you page through a few axial slices you will see that the wm.mgz is connected to the body of the wm in slice 109, disconnecs in 110, then reconnects to a different part in 115, which should never happen

cheers
Bruce
 On Thu, 27 Jul 2017, Jake Rieke wrote:

Hi Bruce,

Thanks for the response. I just uploaded the subject using the ftp file
exchange. The issue is visible in the region close to voxel coordinate [172,
123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I
forgot to mention in my first message that we used a T2 to improve pial
surface after initial running with just the T1.

Thanks again
Jake

Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall VA

Medical Center, 1601 SW Archer Road, Gainesville, FL 32608
Phone: 1-352-376-1611 ext. 5249, E-mail: jakerieke@gmail.com

On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Jake

      usually that means that there is a topology defect that is being
      incorrectly fixed. If you upload the subject and point us at the
      voxel
      coords we will take a look

      cheers
      Bruce

      On Wed, 26 Jul 2017, Jake Rieke wrote:

      > Hello surfers,
      >
      > I'm attempting to extend white and pial surfaces to encompass
      an
      > unrecognized gyrus. The wm.mgz seems include the WM tissue,
      but the white
      > surface does not extend to the WM boundary. I thought this
      might be related
      > to an intensity normalization error and tried using control
      points, but that
      > did not make a big difference in the resulting surfaces. I've
      attached
      > pictures to better illustrate the problem. Thanks in advance
      for your help!
      >
      > Best regards,
      > Jake
      >
      >
      >
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