Hello,
i am trying to get FA value of hippocampus and draw tractography.
After doing all the preprocessing, i did brain parcellation with freesurfer. so i have this template that divide brain in each part.
i used mrcalc to make get hippocampus mask and used mrgrid to make fa.mif and hippocampus template aligned. then with mrstats i got the number (fa value) is this the right way to do it? the reason why i am concerned is that i tried to draw tractography with tckgen i got tractography. is it because i used whitematter fod.mif file?
Hi Minji,
After the DWI preprocessing and FreeSurfer, there is an additional step that is required which may have been missed. The anatomical images (outputs from FreeSurfer) need to be aligned with the DWI, although mrgrid won’t do this. Check out this post on how to do that
After the images are aligned, do mrcalc and mrstats to obtain the FA in the hippocampus (be sure to use images that are indeed aligned 
)
As for hippocampus tractography, this paper might be helpful New insights into anatomical connectivity along the anterior–posterior axis of the human hippocampus using in vivo quantitative fibre tracking | eLife
Hope this helps!
Cheers,
Arkiev