Hi Arman - I changed one of your 5 controls points for the forceps major
to make sure that the initial path is well within the white matter,
following the approach I described to Bryon in my previous email. I'm
attaching the edited text file, please save it in the dlabel/diff/
directory of your subject and rerun the path reconstruction, making sure
that reinit is not set to 1. You can rerun only the fmajor by editing the
pathlist variable in your configuration file.
Hope this helps,
a.y
On Mon, 3 Dec 2012, Arman Eshaghi wrote:
Dear Anastasia,
Thanks for the suggestions. The new control point didn't help. Therefore I
uploaded remaining
images. It would be great if you could have a look again.
All the best,
Arman
On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Arman - One more thing. Do you mind sending me the original (non-skull
stripped) T1 as well? We'd like to test a different registration method
on it.
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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