Dear Anastasia, To 4.: I am comparing TBSS with Tracula results and it seems TBSS now additionaly allows to analyze the partial volumes f1, f2.. of the bedpostX step in a sensible way. My question is: Can I use the bedpostX output from Tracula? I guess so but I am not 100 % sure as with Tracula I have used the T1 weighted image as the volume with no diffusion weighting in order to construct the nodif_brain_mask that is necessary for bedpostX whereas the TBSS processing steps were all run with a mask extracted with BET. Is this different mask a problem for following voxelwise TBSS analysis of the data in all_F*_skeletonised?
Best, Vincent Am 10/11/2013 2:13 PM, schrieb Anastasia Yendiki: > > Hi Vincent - I'll take on the tracula-related parts: > > 2. For tracula, the part of the recon-all output that matters is the > aparc+aseg. The surfaces will play a role only the DWI-to-T1 > registration (assuming you opt to use bbregister). > > 3. It's important to check your DWI data for obvious motion artifacts, > (slices that are much darker than their neighbors). Right now this has > to be done visually, but it's on my list to produce some motion > metrics as part of the preprocessing. > > 4. The ball-and-stick model (that bedpostx fits to your data) is used > by the tractography algorithm in tracula, but there are no stats > produced on the parameters of that model currently. That's something > that can be added in the future as well. Note though that it wouldn't > make sense to just average f1 or f2 over the pathway, because > compartment 1 in one voxel may correspond to compartment 2 in some > other voxel. > > Hope this helps, > a.y > > On Fri, 11 Oct 2013, vbrun...@nmr.mgh.harvard.edu wrote: > >> Dear Freesurfer experts, >> >> I want to do a quality check on our imaging data. I used the >> longitudinal >> stream for SBA and as the first step for the longitudinal white matter >> analysis with TRACULA. >> We had two time points in our study and thus, in the freesurfer output >> directory there are 5 folders per subject (2 cross-sectional runs, 2 >> long >> runs and the base). >> >> 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 >> folders per subject for the SBA? >> 2. Independent of the previous question, for the longitudinal version of >> TRACULA would you recommend to use (all of) the QA_TOOLS on the >> freesurfer >> base folder only / additional folders? >> 3. In addition to the late visual check for well reconstructed pathways >> with freeview, is there another automated possibility to check the >> quality >> of the diffusion weighted images beforehand/do you think this is >> necessary? >> >> 4. On another note: If I understand correctly, in TRACULA bedpostX is >> used >> to reconstruct the pathways but then the mean over the voxels that were >> hit (by the MCMC sampling of the paths) of measures from the tensor >> model >> are taken as outputs. I wonder, is there also the possibility of >> using the >> partial volumes f1, f2,.. as output measures? >> >> Best, >> Vincent >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com _______________________________________________ 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.
