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

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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