Hi Michele,
Don't think there is anything wrong with the attached dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path to your
configuration file.
Right now it reads the path to your file as a flag, which is of course
not what you want.
Best,
Barbara
On 11/09/2014 17:49, Michele Cavallari wrote:
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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