Hi Arman - Yes, this looks like a tough one. This subject has
mega-ventricles and a pretty thin, oddly shaped forceps minor. I can't
actually test if this'll work b/c the bedpost directory is missing from
the uploaded data, but can you please try changing the 2nd control point
in this text file:
dlabel/diff/fminor_PP_avg33_mni_flt_cpts_5.txt
to this:
81 87 25
and rerun the path reconstruction step only for fminor?
Let me know if it works. If it doesn't, send over the bedpostx directory
too and I can try some more things. Thanks!
a.y
On Fri, 30 Nov 2012, Arman Eshaghi wrote:
Dear Anastasia,
Thanks for your response. I have sent a subject that the problem in forceps
minor persists.
What I have done so far was to re-run the pipeline with "reinit=1", check the
eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the tracts look
better for many subjects but this one
still has problems in forceps minor.
Thanks,
Arman
On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi <arman.esha...@gmail.com> wrote:
Dear Anastasia,
Thanks for your response. I have sent a subject that the problem in
forceps minor persists.
What I have done so far was to re-run the pipeline with "reinit=1", check the
eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the tracts look
better for many subjects but this
one still has problems in forceps minor.
Thanks,
Arman
On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Arman - Have you ruled out any issues with the gradient directions? In
situations where the
problem is wide-spread, this seems to be the usual suspect. If you've
checked the eigenvectors
and they're ok, can you send an example case where the problem persists?
You can use this page to
upload a tar ball of all the tracula-related directories of the subject:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Thanks!
a.y
On Mon, 26 Nov 2012, Arman Eshaghi wrote:
Dear all,
I have difficulty sorting out the problem with some tracts in
several subjects,
tracts are incomplete or
missing. As it has come up quite a few times on the list, for this
sort of problem I
have first set
"reinit=1" and then increased control points to 7, and re-ran trac-all with
"-prior"
flag. This has worked
for some tracts in several subjects, however there are a few
subjects that still have
this problem.
It would be great if someone could let me know what else I might be
able to do in
order to correct
missing/faulty tracts in my subjects. (The problem is not limited
to a specific
tract, it varies in
different subjects)
All the best,
-Arman
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