Re: [Freesurfer] problems with tracula pre-processing (bvecs)

1 Oct 2014

      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 <
ayendiki@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.Watson@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.michele@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.michele@gmail.com> wrote:
      Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson <
Christopher.Watson@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.michele@gmail.com> wrote:
      Thanks! it's running...
On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp <
bakk.hbg@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 <
ayendiki@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
        <ayendiki@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
                    <ayendiki@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, lshih@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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Re: [Freesurfer] problems with tracula pre-processing (bvecs)