Plotting AFD of specific fixels


I ran the FBA analysis pipeline up to generating streamlines for tractography. I’ve got a directory named ‘fd’ under my ‘template’ directory, containing what I assume are files containing the FD of each fixel for every subject, as well as a directions and index file. I’m wondering how I can track the FD of a certain fixel across all subjects? Is there a way to check which line on the fixel data file belongs to which fixel, and in which voxel?



Hi Ana,

To understand the mapping between the fixels present in the template and how they are stored on the filesystem, see this section of the documentation.

There are all sorts of ways that it would be theoretically possible to provide a more visual interaction with the fixel data (e.g. I’d love to be able to edit fixel ROIs within mrview), but our development resources are spread pretty thin at the moment. But the combination of the index and directions image should be sufficient to at least infer the index of one specific fixel of interest.

From there you could interrogate the raw values within the fixel data using something like (executed from inside the fixel directory):

for_each -exclude index.mif -exclude directions.mif * : \
mrconvert IN -coord 0 ##### - "|" mrdump - ">>" fixeldata.txt

Replace “#####” with the index of the fixel in which you are interested.


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Thank you so much!