Tried...unfortunately it didn't improve On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson < christopher.wat...@childrens.harvard.edu> wrote:
> 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. > > [image: Inline image 2] > > > > > > On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari < > cavallari.mich...@gmail.com> wrote: > >> Thanks! it's running... >> >> On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp < >> bakk....@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 < >>> ayend...@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 < >>>>> ayend...@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 >>>>> <ayend...@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, ls...@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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