Hello FSL experts,

I had a few more questions about local probabilistic tractography in probtrackx.

1.) I am still not sure how best to view the tracts that I have made in fslview. The tracts are currently in diffusion sapce.

Currently I am using the command:

fslview dmri.bedpostX/mean_f1samples.nii.gz dmri.bedpostX/LBLA_LvmPFC/fdt_paths.nii.gz -l Red

Is it correct to use the mean_f1samples.nii.gz from bedpost as the underlay? I think it would be helpful to use the 3D Viewer, but I am unsure what parameters to use.

2.) I would like to use the following normalization procedures as conducted by Baur (2012), unless you think there are more optimal procedures? I am not sure how to go about doing this.

After tractography, within-tract probabilistic values were normalized on the individual level by

dividing, voxel-wise, the number of streamlines passing through the voxel by the total number of obtained streamlines (“waytotal”) (52). Subsequently, statistically normalized tracts were thresholded at .05, incorporating only those voxels where at least5%of the total

number of streamlines passed.

3.) Do group level analyses need to be conducted in standard space (MNI space)?

Say for example is I wanted to correlate individual differences in anxiety levels with FA values of a tract connecting the basolateral amygdala and ventromedial prefrontal cortex?

Thanks again, I appreciate any advice you can give me!

Emily