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
On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
hi ay,
i'll look into the orientations a little later tonight, but here is V1
overlaid on FA for preflip and postflip execution of dtifit.
cheers,
satra
On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:
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 preprocessing. Is
there any chance that they're not?
Looking at the sample data set that you sent me, I can only see
what came out of your preprocessing and not what went in. I'm
assuming that this is from the standard Siemens 60 direction
sequence, and it has 57 directions b/c 3 of them were thrown out
by your preprocessing. I don't know which directions were thrown
out obviously, but the first 2 directions in your gradient table
are:
-0.99699027939850948 -0.057720153020443053 0.051758263409041924
0.63287878858184599 0.066164234845749903 0.77141869630019422
The first two directions in the Siemens 60 direction gradient
table are:
1.0000000000 0.0000000000 0.0000000000
0.5867917880 -0.3765825401 -0.7168409782
There's not only a small adjustment of the direction but also a
sign change there. So I'd look into that.
Let me know if any of my assumptions about your original data is
wrong.
a.y
On Tue, 2 Jul 2013, Satrajit Ghosh wrote:
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 eddy correction,
discards bad directions,
reorients the gradients appropriately and generates
a report of the quality)
2. run tracula on this nifti file
observation:
when i run fsl/dtifit on the same nifti file + bvec
+ bval, i get the proper
orientation for eigvec1 lines. however, when i feed
this into tracula, the
output of the dtifit step looks terrible - i.e. the
lines are not oriented
as how one might expect water to diffuse.
suspicion:
although i have not reached the crash yet, i believe
it might be related to
this fact that the gradients are not oriented
properly relative to the
volume.
i also suspect that this has something to do with
the flip4fsl step inside
tracula, which is possibly unnecessary because fsl
already likes the input
files. but it seems this step is encoded quite
heavily within the trac-all
scripts.
questions:
a. is there a quick way to turn the flip4fsl step
off?
b. alternatively do you have any suggestions for
what to do here?
the whole point of running through DTIPrep is to
clean up the data before
giving it to tracula or other programs, so i would
really like to keep that
step.
cheers,
satra
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