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

                  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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