Dear all, What does this mean? That tracula is more robust when running it seperately for the tracts I am interested in? Thanks, Barbara
On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari < cavallari.mich...@gmail.com> wrote: > 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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