Dear friends,
I am a raw recruit in the field of neuroimaging. Thank you very much kind support from this website! Now I have a Gordian knot and really hope that you can give me kind guide.
I have finished preprocessing and TBSS of DTI data using FSL. In addition, I have created a mask of thalamus and superior temporal gyrus according to HarvardOxford atlas(seperate thalamus, seperate superior temporal gyrus and combination of thalamus and superior temporal gyrus). And now I want to obtain the FA value of white matter fiber between thalamus and superior temporal gyrus. But this fiber is not given by FSL XTRACT, JHU atlas as well as other atlases. Could you be so kind to give me some clues to settle this question? Though I hope to use FSL to solve this problem as well, if there is some other tool box can help, I am willing to change my toolbox as well.
Thank you for your precious time!
Hi!
If your wanted tract between these two regions is not available in any atlas you have to create it by yourself. The keyword here is tractography. If you already are in the "FSL world", you could use FSL's bedpostx and probtrackx. Any other toolbox that is able to create some kind of a binary or even probabilistic voxel map (tractogram) is also more than valid, as long as this map can be used in subject's diffusion space (preferable) as a region-of-interest to extract, e.g., average FA.
Best,
Martin
Can you kindly provide link to the software you're using for processing vendor-agnostic raw DTI data?
Do you mean FSL? It's https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
Or as an alternative, rather easy to use and quite versatile - DSI Studio: https://dsi-studio.labsolver.org
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