Hello Afni Experts,

I have some questions regarding diffusion tensor imaging analyses. I am quite new to this, so I appreciate your patience.

I have done all of the initial preprocessing steps (convert DWI to nifti files, eddy current correction, create a brain mask from low-b diffusion images) as well as bedpostx (Bayesian Estimation of Diffusion Parameters Obtained using Sampling Technique, runs Markov Chain Monte Carlo sampling to build up distributions on diffusion parameters at each voxel. It creates all the files necessary for running probabilistic tractography) all in FSL.

I would like to do the next analysis steps in AFNI if possible. My goal is to track the basolateral amygdala to the ventromedial prefrontal cortex as well as the centromedial amygdala to the anterior midcingulate cortex. I have rois of each of these structures based on atlases. I have converted these rois into each subject's diffusion space. Would I do this in FATCAT? If so, can you give me some idea of where to begin? What outputs from bedpostx might I need to input?

Then after I have created these tracts, I assume I need to some normalization and thresholding procedures. For example, the paper that I am basing my analyses of did the following : After tractography, within-tract probabilistic values were normalized on the individual level bydividing, voxel-wise, the number of streamlines passing through the voxel by the total number of obtained streamlines (“waytotal”). Subsequently, statistically normalized tracts were thresholded at .05, incorporating only those voxels where at least 5%of the total number of streamlines passed.

Then I would like to extract diffusivity measures (FA, MD, RD, etc)? Would I utilize 3dcalc for this? Then for visualizing the tracts, would SUMA be my best option?

Thanks so much and sorry for such a long winded email!

Emily