Hi Satra - There are 2 ways to put things in proper orientation for fsl
tools:
1. L-R flip the gradient vectors: This is a hack, in the sense that it
anticipates that FSL will treat your volume as L-R flipped when it has a
certain type of orientation, but now you've broken your bvecs for
Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl
will do is convert it to LAS, and perform the same conversion on the
gradient table that you provide. This of course assumes that
dwi_orig.nii.gz and your gradient table are consistent as they come out of
your custom
Hi Satra - What you're showing in the screenshots would be consistent with
a L-R flip of the gradient directions, which is what my comparison of your
gradients to the original Siemens gradients indicated. (Assuming the data
was acquired with the standard Siemens 60 gradient directions.)
a.y
hi ay,
so this is what i did. i flipped the gradient LR intentionally, ran
flip4fsl and then dtifit and now the eigenvec 1 looks good, but not if i
run dtifit prior to flip4fsl.
but this brings me back to my original point which is that my image and the
gradients are (i think) already in proper
hi anastasia,
i'm trying to debug a seg fault that some folks are seeing deep into a
tracula run.
process:
1. feed dicoms to a script that runs DTIPrep and outputs a nifti file,
bvec, bval
(among checking for many artifacts, this reduces the b=0 volumes to a
single registered mean volume, runs
