I'm not positive of the argument for doing it this way, but in the past I've been advised by this list to use ApplyXFM_gui and diff2str.mat to align dti_FA to my T1 image. I think it was decided that this was the best way since it would preserve the resolution of fdt_paths (my T1 slices are 1mm thick whereas my DTI slices are 2mm thick).
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Jeremy Young
Sent: Tue 4/14/2009 3:21 PM
To: [log in to unmask]
Subject: [FSL] tracking in T1, and pulling out expected FA values
Hi all,
After running probtrackx tracking in T1 space, I want to pull out
expected FA values by multiplying the dtifit_FA.nii.gz volume with
the normalized and thresholded path volume using fslmaths. The
problem is dtifit_FA is in FA space and the path is in T1 space.
What's the appropriate thing to do, flirt the dtifit_FA into T1
space or flirting the path into FA space?
I've tried it both ways and the #'s come out differently but not
an order of magnitude differently.
Thanks for your help!
Jeremy
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