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Hi
when you use avwswapdim a b c, then you have to:
- replace the first line of your bvecs by the a-th line
- replace the second line by the b-th line
- replace the third line by the c-th
(if a,b,c contain '-' sign, then add a '-' sign to the corresponding line)

You don't have to normalise your bvecs if you use dtifit, but you have to do it if you use bedpost (will be changed in the next release).

Your bvecs contain a comma (,) instead of a dot (.) ie use French notation (and probably German?). You should change all your ',' into '.'

Attached are the reoriented and normalised bvecs if you want to compare with what you would obtain (you shouldn't be using Excel)

Cheers,
Saad

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On 25 Jun 2007, at 08:28, Agnieszka Burzynska wrote:

Dear all,
I had to reorient the data.nii of one brain using avwswapdim  z -x y. Now
comes the bvecs reorientation. I read bvec emails in archives, but did not
find answers to all my questions.

I attach a part of Excel file with imported data from my bvecs
(1x b=0, 12
directions b=1000). You can see how the ´bad´ bvecs looked like and how I
plan to change them - Am I correct? OR: can I first normalize them and then
rotate?

Also, I show two example bvecs contents of the correctly oriented data -
they look still quite different from the ´corrected´ bvecs. Will it still be
fine?

As you see, I did not normalize them yet, but still could run DTIFit. Is it
´normal´? Is it also ok that the values are not the same in all files?

On the bottom (yellow) of the file you will find the first try to normalize
bvecs: I get the values 1, 0, -1 only after rounding it up to 0 decimal
places (orange). Is such outcome the right one?

And: thank you for all advices: I do not always respond directly, not to
overload the mailing list with too many ´Thank you`s. But I am really
grateful.

Best,
Aga



<bvecsAga.txt>

 
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Saad Jbabdi, 
Postdoctoral Research Assistant,  
Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222545  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
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