Hi Tyler - In general this means that for some reason the pathway doesn't
move at all from the location where it's initialized when the algorithm is
run. There are a few different reasons why that'd happen, the mask being
only one of them.
If you could find the dmri_paths command line in
Thanks, Tyler. It looks like the initial pathway is problematic in that it
goes off the white matter (look at the Reject due to lines in the log
for exact voxel coords where this happens).
This could mean that the subject is not well aligned to the atlas in that
area, or that you just got
Anastasia,
Rerunning with the reinit = 1 option worked great. One last question. If I
want to compare tracts across subjects, should I rerun every subject with
the reinitialization, or is it ok to only rerun the subjects/tracts that
need it? Thanks for all you help.
-Tyler
Thanks, Tyler. It
Great! You just need to rerun cases where the original initialization was
bad.
On Thu, 1 Dec 2011, bla...@artsci.wustl.edu wrote:
Anastasia,
Rerunning with the reinit = 1 option worked great. One last question. If I
want to compare tracts across subjects, should I rerun every subject with
Hi List,
I recently ran a group of around 70 subjects through trac-all. I have started
to check the results, and have noticed that Tracula will often produce a tract
with a really small volume and a posterior distribution that consists of just
0s and 1000s. When this occurs, the end point
Hi Tyler - Sometimes this happens if the brain mask (which will come
either from the FS recon or from the DWIs themselves, depending on your
settings) is missing part of that tract (usually one of the end region).
Have you checked your brain masks?
a.y
On Wed, 30 Nov 2011, Tyler Blazey
Hi Anastasia,
Thanks so much for your quick reply. As far as I can tell the masks seem fine.
There was a small amount of erosion around the edge of the brain when the recon
mask was used. However, the end points of the tract were still within the mask.
Just in case I reran trac-all with the
