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:
- 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).
- 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.
- 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, vbrunsch@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).
- 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?
- 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
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