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
[image: 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:
- 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
- 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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