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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