it depends. In this case you want to erase as it creates an incorrect connection. In others you want to add if there is an incorrect break
On Fri, 28 Jul 2017, Jake Rieke wrote:
Thanks, Bruce and Douglas! Looking at the surface prior to the topology
correction step has been very helpful. I can see the region you pointed out
- where the wm.mgz connects to the body of the wm, disconnects, and then
reconnects at a different spot. I'm having some trouble implementing the
manual edits to the wm.mgz.
Part of the problem is that I'm still training my eye to differentiate GM
and WM (especially in cases with thin tracts or partial voluming), but this
gives me a great place to start.
I'm wondering, in general, is the idea to erase or add voxels in the wm.mgz
where the defects are located? In other words, defects can be interpreted as
areas of misclassified as WM? In this case, it seems that I need to focus on
deleting voxels in the wm.mgz that are incorrectly segmented.
Thanks,
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 Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
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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