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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