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.michele@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.michele@gmail.com> wrote:
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson < Christopher.Watson@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.michele@gmail.com> wrote:
Thanks! it's running...
On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp < 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> 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> 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 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 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. Thank you. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the > person > to whom it is > addressed. If you believe this e-mail was sent to you in > error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail > was sent > to you in error > but does not contain patient information, please contact > the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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