Hi Anastasia,
I am probably doing something wrong with the syntax of the
dmrirc file.
I get this error message
trac-all -prior
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
ERROR: flag
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
unrecognized
-prior
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
Could you please check the attached file?
On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu
<mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
Thanks, Michele. Hard to tell what's causing this,
perhaps a bit of distortion orbitofrontally. You may be
able to fix this type of thing by reinitializing the
tract reconstruction: Add "set reinit = 1" to your
configuration file, set the pathlist to include only the
left and right uncinate, and then rerun the -prior and
-path steps of trac-all on this subject.
On Wed, 10 Sep 2014, Michele Cavallari wrote:
uploaded (and activated).Thanks!
On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu
<mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
Hi Michele - The anatomical segmentation does
look good, but from the
screenshot the DWI data seems to be noisy in
the orbitofrontal area, which
may be affecting the uncinate. It's hard to
tell just from one slice.
If you upload all the tracula output
directories of this subject (dmri,
dmri.bedpostX, dlabel, dpath) for me here, I'll
take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
a.y
On Wed, 10 Sep 2014, Michele Cavallari wrote:
Hi Anastasia,I completed the tracula
processing.
By looking at the tractography results in
the viewer I noticed
that the uncinate
fasciculus is pretty small (see attached
screenshot). It
actually appears as a small
blue dot. And the problem is both on the
left and right side.
The other tracts look
fine. I played with threshold, but the
size didn't increase. So,
I guess that something
wrong happened with the tractography of
that particular bundle.
I checked the aparc+aseg
output (attached): it seems right to me,
but could you please
double-check?
Let me also know if you have any
suggestions, and if you need
more information or output
files.
Best,
Michele
Inline image 1
On Thu, Sep 4, 2014 at 11:55 PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu
<mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
Hi Ludy - If your gradient table is
formatted in 3 rows
you need to
either:
1. Convert it to 3 columns so you
can use it with the 5.3
version of
tracula, which requires the
gradient table to be formatted
in columns
OR
2. Download the tracula update that
can use gradient
tables formatted in
rows
Hope this helps,
a.y
On Thu, 4 Sep 2014,
ls...@bidmc.harvard.edu
<mailto:ls...@bidmc.harvard.edu> wrote:
> Hi,
>
> I was having similar errors as
Michele Cavallari
regarding "error reading
/path/to/subject/dmri/dwi_frame," but I'm not sure it's
related to my bvecs
file. I did try reconfiguring my
bvecs file into columns
instead of row just
in case, but that didn't solve the
problem. It really just
looks like it
can't find the dwi_frame file after
the mri_concat
command.
>
> I am attaching my trac-all.log
and config file.
>
> Running Freesurfer 5.3 on Macbook
OS 10.7.5. The bvecs
files were
generated after I converted my
dicoms to nifti using
dcm2niigui (GE
scanner).
>
> Can anyone tell me how dwi_frame
is generated?
>
>
> Ludy
>
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