Hi Emily,
1. That's fine because the BET-based mask is not used by default in the the tractography. The brain mask from the freesurfer segmentation of the structural scan is used instead.
2. To check the diffusion-to-anatomical registration, you can look at the aparc+aseg registered into diffusion space, i.e., from the dlabel/diff directory, overlaid onto the FA map. It's also important to check that the gradient table is correct by looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines. Assuming the protocol is the same for all subjects, you just need to do this latter check for one of your subjects only.
3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of specific tracts. Information on the anatomical regions that these tracts go through or next to is derived from a set of training subjects. See our paper for more info:
http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstrac...
Hope this helps, a.y
On Thu, 10 Jul 2014, ebelleau@uwm.edu wrote:
Hello,
I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me.
1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files.
I looked at my eddy current corrected diffusion data (which I believe is in data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed that the no_dif_brain_mask does not cover very well for some of my subjects. Should I individually tailor the Fractional Intensity Threshold for BET mask extraction from low-b images at the prep stage?
2.) In general what files should I be checking at each phase (prep, bedpost, path)?
3.)How do you generate the whole-brain ROIS to guide the tractography (is the white matter mask that is generated at the prep phase involved)?
Thanks,
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer