Hi Vincent,
I had the same problem before and would really appreciate advice from an FSL expert on whether there is a correct/better way to fix this problem.
This is what I did to fix the orientation:
I swapped around the rows that represent the x, y and z coordinates in the bvecs file before running DTIfit.
(It is easier to see when you transpose the bvecs file from rows to columns in Matlab. When in directory containing my bvecs file I just typed load bvecs, and then typed
bvecs').
In my data the initial colour orientation in FSL was:
X(anterior-posterior; red) y (inferior-superior, green) z (left-right,
blue). I made a new bvecs matrix in Matlab representing the same
columns of bvecs but in the order z x y - this gave the right
orientation; (L-R red, A-P green, I-S blue). I used the command line
bvecs = [bvecs(:,3), bvecs(:,1), bvecs(:,2)]. I copied this matrix
into a new txt file and saved it as the new bvecs file
ready for bedposting/DTI fit.
Also, after doing this, the red left-right
fibres were going the wrong direction, which meant that the
inferior-superior fibres were flipped (ie. the positive and negative
directions were the other way around). I swapped the plus and minus signs in front of each value of the third
bvec column (z-direction), which fixed the problem.
It might take a few times of checking all options (ie swapping columns in different ways and using +/- in front of
each column) to see what works for your data.
I'm not sure if this is the way to go but it seemed to work for my data.
Hope this helps!
Kristin
________________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Vincent Koppelmans <[log in to unmask]>
Sent: 13 January 2014 22:48
To: [log in to unmask]
Subject: [FSL] DTIFIT: orientation issue
Dear FSL experts,
I have DWI data that was (unintentionally) acquired from left to right.
When I use dtifit for tensor fitting and modulate the resulting FA image with the V1 image, the corpus callosum appears green.
What should do to fix this?
Thanks,
Vincent
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