Well, if you do that you may as well use the unrotated bvecs, no?
Cheers-
Andreas
________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von wlzhu [[log in to unmask]]
Gesendet: Freitag, 12. März 2010 04:18
An: [log in to unmask]
Betreff: Re: [FSL] rotating bvecs
I have modified it to fit for file name is absolute path in *.ecclog.
For use, we have two acquisition each subject and each has the same bvecs.
We first merge the second image to the first one. Then perform eddy correct with reference of the b0 in first image.
Next split the corrected image to 2 images, finally average them.
The question is ,although two images have same bvecs, after using rotate_bves, the two bves are not same(slightly different).
Is it acceptable to use the first rotated bvecs as the gradient of averaged image.
thanks
wanlin
On Fri, Mar 12, 2010 at 11:18 AM, Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Gad,
You might want to just use the existing fix described in the
mailing list. This bug was noted and a fix posted which just
involved changing one line. I've attached the fixed version.
Note that this version behaves like the old one and keeps
the naming of the bvecs file consistent so that it will work
with other FSL tools such as bedpostx.
All the best,
Mark
On 11 Mar 2010, at 23:23, Dave Deriso wrote:
Hi Gad,
I had the same promlem, so I just rewrote the script. It works pretty well for me. Give this a whirl and please be sure to let me know if it works without error!
**Make sure you are in the same directory as the files when you run it.
Attached is a zip file that contains:
1. rewritten script "rotate_bvecs2"
2. sample data "test.bvec" and "test.ecclog" these work reliably well for me
3. a sample output file "test_rot.bvec"
4. a text file with what the terminal should print
Good luck!
Best,
Dave Deriso
UCSD Psychiatry
On Thu, Mar 11, 2010 at 2:04 PM, Gad Klein <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I am following the instructions on the FSL site to pre-process diffusion
data prior to bedpostX. After eddy current correction worked nicely I tried
to use the provided script to rotate by bvecs, but kept getting an error
message. On the site the script is written as:
rotate_bvecs <4doutput>.ecclog <bvecs>
so I entered: rotate_bvecs
/home/gklein/probDTI/DiffData/ambersleydata/DTI_Sat33+5/data.ecclog
/home/gklein/probDTI/DiffData/ambersleydata/DTI_Sat33+5/RESUlug4s010a1001.bvec
and got this error message: [: 9:
/home/gklein/probDTI/DiffData/ambersleydata/DTI_Sat33+5/RESUlug4s010a1001:
unexpected operator
/usr/share/fsl/bin/rotate_bvecs: 21: Syntax error: "done" unexpected
(expecting "fi")
Am I entering the bvec file incorrectly or something. Any help would be
appreciated. Thanks.
-Gad
<test_rotate_bvecs.zip>
