errata corrige: it did work! I had to re-run the whole thing including only that specific tract...and eventually it worked.
On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari < cavallari.mich...@gmail.com> wrote: > 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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