Hi Anastasia, thanks for your feedback. I checked both te aparc+aseg and the
diffusion images. There
is some underestimation of left insula and left temporal pole in the mask,
corresponding to quite
large missing (0 value) areas in the FA maps.
I tried to re-run the -prep step using the "-prior" option and with no success:
still getting a
'segmentation fault' error message (log and error files attached).
Is there anything else I can try to analyze this case without having to re-run
the
segmentation/parcellation?
And are there ways to improve the parcellation in those regions?
Thanks
On Wed, Sep 24, 2014 at 6:11 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Michele - It seems like it's failing in the right uncinate again. From
the error, I
would guess that part of that tract is getting left out of the brain mask
or something of
that sort. Can you please check how that area looks in the aparc+aseg and
in the diffusion
data?
a.y
On Thu, 18 Sep 2014, Michele Cavallari wrote:
Hi, I am having problems with tracula pre-processing for a case of a
series I am
analyzing. The processing worked without errors for two out of three
cases I was running at the same time. I received a 'segmentation fault'
error. I
checked the FreeSurfer recon-all output, and it was completed
without errors. I tried to re-process the case alone: got the very same
outcome.
I am enclosing the log file of the tracula processing of the case that's
giving me
an error.
Let me know if you need more information/files.
Thanks,
-Michele
On Tue, Sep 16, 2014 at 6:11 PM, Chris Watson
<christopher.wat...@childrens.harvard.edu> wrote:
I don't think that would change the results (significantly), so you
would just
be wasting processing time. It depends on the quality of
your data. In this thread, as Anastasia said earlier, there is
distortion
around the L orbitofrontal cortex, which may have caused the
problem Michele was having (reconstructing the L uncinate).
But if you're *only* interested in a subset of the available
tracts, you
should probably comment out the others, if you want to save
time.
On 09/16/2014 07:18 AM, Barbara Kreilkamp wrote:
Dear all,
What does this mean? That tracula is more robust when running it
seperately
for the tracts I am interested in?
Thanks,
Barbara
On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari
<cavallari.mich...@gmail.com> wrote:
errata corrige: it did work! I had to re-run the whole thing
including
only that specific tract...and eventually it
worked.
On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari
<cavallari.mich...@gmail.com>
wrote:
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson
<christopher.wat...@childrens.harvard.edu> wrote:
You can try just re-running "trac-prep -prior" and "trac-paths" for
the L
uncinate and no other tracts
On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I re-ran the case with the set reinit option. It "half"
worked!...in the
sense that the new results
show the left uncinate right, but the right-side one is still a dot
(see
screenshot of the brain view from
the bottom). Any further suggestion?
Thanks.
Inline image 2
On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari
<cavallari.mich...@gmail.com> wrote:
Thanks! it's running...
On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp <bakk....@googlemail.com>
wrote:
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> 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> 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> 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 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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