Hi, I am having problems with tracula pre-processing for a case of a series I am analyzing. The processing worked without errors for two out of three cases I was running at the same time. I received a 'segmentation fault' error. I checked the FreeSurfer recon-all output, and it was completed without errors. I tried to re-process the case alone: got the very same outcome. I am enclosing the log file of the tracula processing of the case that's giving me an error. Let me know if you need more information/files. Thanks, -Michele
On Tue, Sep 16, 2014 at 6:11 PM, Chris Watson < Christopher.Watson@childrens.harvard.edu> wrote:
I don't think that would change the results (significantly), so you would just be wasting processing time. It depends on the quality of your data. In this thread, as Anastasia said earlier, there is distortion around the L orbitofrontal cortex, which may have caused the problem Michele was having (reconstructing the L uncinate).
But if you're *only* interested in a subset of the available tracts, you should probably comment out the others, if you want to save time.
On 09/16/2014 07:18 AM, Barbara Kreilkamp wrote:
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. 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