Hi Sue,

Atlasquery, like any atlas reporting tool, is meant to be used as a helper. You can always overlay your results to an MNI image, open an anatomy textbook, and use the anatomical references to identify the regions.

You can as well use tools such as fslstats and fslmaths and shell scripting to define other indices of overlap, e.g., what is the percentage of the tract that is within the mask? In your case that quantity may well be a high number, even 100%...

All the best,

Anderson

On 15 January 2018 at 00:53, Wang ChenXi <[log in to unmask]> wrote:

Hi experts,

I am a little confused about how to report TBSS results, below are questions:

Q1.

I have noticed there is command, atlasquery -a "JHU ICBM-DTI-81 White-Matter Labels" -m Sig_mask.nii.gz, and as the wiki says, it gives the (average) probability of a voxel or mask being a member of the different labelled regions within the atlas, if a mask is used then the probability is averaged over all the voxels in the mask. Does it mean the percentage of the mask that belongs to each or specific WM tract? If so, i don't think it always makes sense. See that for example, for tract A it reports a 0.1%, it seems that i don't need to report this result because of the low percentage, however, a possible situation is that volume (tract A) / volume (mask) is equal to 0.1%, which means tract A is a very important location that i can't ignore. Is this idea correct and are there any other tool to report TBSS results?

Q2.

Since the "JHU ICBM-DTI-81 White-Matter Labels" atlas does not cover the whole WM skeleton, "atlasquery" often reports unclassified percentage which can reach to 50%, what can i do to deal with it?

Sincerely,

Sue