fortunately at least for your cases it's simple... you actually have a
"B0" + 6 gradient directions... fsl expects its BVECS file to be in
rows, not columns
so your bvecs would look like
bvecs
0 1000 1000 1000 1000 1000 1000
bvals
0 1 -1 0 0 1 -1
0 0 0 1 1 1 1
0 1 1 1 -1 0 0
Basically Ijust transposed your gradients from columns to rows, and
prepended a "0" for the b0 image that should precede the vectors...
Also an important tip-- assuming your running this on a linux
machine-- edit/create the file using linux... if you create the files
on a windows machine, sometimes extra characters gets appended at the
end of each line that at least used to make bedpostx not work
properly..
also once your directory contains the
data.nii.gz
nodif_brain_mask.nii.gz
bvecs
bvals
(I think I got all the files)
run bedpostx_datacheck and it will make sure your files are in the
right format and make sense... i.e. if your data volume has 67
volumes... but your bvecs only contains gradients... it will notice
the inconsistency and report an error
> 1 0 1
> -1 0 1
> 0 1 1
> 0 1 -1
> 1 1 0
> -1 1 0
On Mon, Jan 10, 2011 at 8:35 AM, Ivan Maximov <[log in to unmask]> wrote:
> Dear Colleagues,
>
> Sorry for the newbie's question.
> I would like to understand how to build up the bvecs file from scratch. The info from DFT webpage is still dark for me. Probably,
> someone could help me.
>
> I have bvals as following: 0 1000 1000 1000 1000 1000 1000
> I means one acquisition for 6 directions.
> The gradient directions are:
> 1 0 1
> -1 0 1
> 0 1 1
> 0 1 -1
> 1 1 0
> -1 1 0
>
> How to construct the bvecs?
>
> Thanks very much in advance
> Ivan
>
--
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine
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