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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