11 Sep
2014
11 Sep
'14
4:56 p.m.
You can try just re-running "trac-prep -prior" and "trac-paths" for the L uncinate and no other tracts
On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I re-ran the case with the set reinit option. It "half" worked!...in the sense that the new results show the left uncinate right, but the right-side one is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks.
Inline image 2
On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari <cavallari.michele@gmail.com mailto:cavallari.michele@gmail.com> wrote:
Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com <mailto:bakk.hbg@googlemail.com>> wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote:Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add "set reinit = 1" to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: 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 <mailto: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 <mailto: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 > > This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. 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