Re: [Freesurfer] Tracula reconstructed tracts quality
Hi Anastasia, Thanks for taking a look and point that out. I'll have to be more careful in checking the source images, instead of going by the notes (and memory of events years past) left by the previous engineers on the project.;) -Peggy On Mon, Sep 8, 2014 at 6:21 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Peggy - I looked at the data. Unfortunately, the voxel size is > 0.9x0.9x4 in the first time point and 0.9x0.9x5.2 in the second. So not > only is the resolution extremely anisotropic, which is problematic for > tractography, but it's also different between scans, which almost > guarantees that you will find longitudinal changes (except you won't know > if it's because the brain is changing or the scan is changing). > > Finally, the 12 directions that you have may not be sufficient to fit a > crossing-fiber model like the ball-and-stick model, which may explain the > noisy output. > > a.y > > On Mon, 8 Sep 2014, Peggy Skelly wrote: > > > Hello Tracula experts, > > I was wondering if you could comment on the quality of the tracts > reconstructed with our > > 1.5T data. These 2 files are from the same subject at 2 timepoints, > processed in the > > longitudinal stream. > > > > Is much of the non-smooth look of the tracts due to the resolution of > the dwi scans > > (1.8x1.8x4mm)? > > What could be the source of the diagonal lines/gaps in the tracts seen > in tp1 when > > viewed from above? > > > > Thanks, > > Peggy > > > > > > > ___ > 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.
Re: [Freesurfer] Tracula reconstructed tracts quality
Hi Peggy - I looked at the data. Unfortunately, the voxel size is 0.9x0.9x4 in the first time point and 0.9x0.9x5.2 in the second. So not only is the resolution extremely anisotropic, which is problematic for tractography, but it's also different between scans, which almost guarantees that you will find longitudinal changes (except you won't know if it's because the brain is changing or the scan is changing). Finally, the 12 directions that you have may not be sufficient to fit a crossing-fiber model like the ball-and-stick model, which may explain the noisy output. a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: > Hello Tracula experts, > I was wondering if you could comment on the quality of the tracts > reconstructed with our > 1.5T data. These 2 files are from the same subject at 2 timepoints, processed > in the > longitudinal stream. > > Is much of the non-smooth look of the tracts due to the resolution of the dwi > scans > (1.8x1.8x4mm)? > What could be the source of the diagonal lines/gaps in the tracts seen in tp1 > when > viewed from above? > > Thanks, > Peggy > > > ___ 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.
Re: [Freesurfer] Tracula reconstructed tracts quality
Hi Peggy - It's hard to diagnose the problem by seeing only the tracts and not the rest of the data, but this does look very strange. 1.5T is not a problem, but anisotropic resolution is not optimal for tractography, as it can bias the amount of diffusion measured in the direction that the voxels are larger. If you upload the entire data set (all the tracula directories: dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a closer look. https://gate.nmr.mgh.harvard.edu/filedrop2/ a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: > Hello Tracula experts, > I was wondering if you could comment on the quality of the tracts > reconstructed with our > 1.5T data. These 2 files are from the same subject at 2 timepoints, processed > in the > longitudinal stream. > > Is much of the non-smooth look of the tracts due to the resolution of the dwi > scans > (1.8x1.8x4mm)? > What could be the source of the diagonal lines/gaps in the tracts seen in tp1 > when > viewed from above? > > Thanks, > Peggy > > > ___ 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.
