Re: [Freesurfer] TRACULA tract path failure

Thank you for correcting this. This in fact works. Alternatively after re-running the pipeline with reinit=1 for so many times, as it tried different initialization each time I managed to get the tract.

All the best, -Arman

On Fri, Dec 21, 2012 at 12:56 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Arman - I changed one of your 5 controls points for the forceps major to make sure that the initial path is well within the white matter, following the approach I described to Bryon in my previous email. I'm attaching the edited text file, please save it in the dlabel/diff/ directory of your subject and rerun the path reconstruction, making sure that reinit is not set to 1. You can rerun only the fmajor by editing the pathlist variable in your configuration file.

Hope this helps, a.y

On Mon, 3 Dec 2012, Arman Eshaghi wrote:

Dear Anastasia,

...

Thanks for the suggestions. The new control point didn't help. Therefore I uploaded remaining images. It would be great if you could have a look again.

All the best, Arman

On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

  Hi Arman - One more thing. Do you mind sending me the original

(non-skull stripped) T1 as well? We'd like to test a different registration method on it. Thanks!

  a.y

  On Fri, 30 Nov 2012, Arman Eshaghi wrote:

        Dear Anastasia,
        Thanks for your response. I have sent a subject that the

problem in forceps minor persists. What I have done so far was to re-run the pipeline with "reinit=1", check the eigenvectors, increase control points, switch off brain anatomical mask in dmric. It made the tracts look better for many subjects but this one still has problems in forceps minor.

        Thanks,
        Arman


        On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi
        <arman.eshaghi@gmail.com> wrote:
              Dear Anastasia,
              Thanks for your response. I have sent a subject that the
        problem in forceps minor persists.
        What I have done so far was to re-run the pipeline with

"reinit=1", check the eigenvectors, increase control points, switch off brain anatomical mask in dmric. It made the tracts look better for many subjects but this one still has problems in forceps minor.

        Thanks,
        Arman


        On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki
        <ayendiki@nmr.mgh.harvard.edu> wrote:

              Hi Arman - Have you ruled out any issues with the

gradient directions? In situations where the problem is wide-spread, this seems to be the usual suspect. If you've checked the eigenvectors and they're ok, can you send an example case where the problem persists? You can use this page to upload a tar ball of all the tracula-related directories of the subject:

        https://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**

html https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

              Thanks!
              a.y

              On Mon, 26 Nov 2012, Arman Eshaghi wrote:

                    Dear all,
                    I have difficulty sorting out the problem with

some tracts in several subjects, tracts are incomplete or missing. As it has come up quite a few times on the list, for this sort of problem I have first set "reinit=1" and then increased control points to 7, and re-ran trac-all with "-prior" flag. This has worked for some tracts in several subjects, however there are a few subjects that still have this problem.

                    It would be great if someone could let me know

what else I might be able to do in order to correct missing/faulty tracts in my subjects. (The problem is not limited to a specific tract, it varies in different subjects)

                    All the best,
                    -Arman




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