Below is a simple matlab script that extracts the b=0 and b=1000 bvals and bvecs. The script merges b=0 and b=1000 bvals/bvecs at the end and saves them as bvals_b1000 and bvecs_b1000, and I use fslmerge to merge the b=0 and b=1000 volumes so that all of the files correspond.

Joe

%hcp_b1000_bvecs_bvals.m

workdir='/work/ics/data/projects/banichlab/studies/hcp/dti';

cd(workdir)

[status,list]=system('ls */T1w/Diffusion/bvals | cut -d ''/'' -f1')

subjs=str2num(list);

for i=1:size(subjs,1)

cd([workdir '/' num2str(subjs(i)) '/T1w/Diffusion'])

% Read bvals and bvecs text files

num2str(subjs(i))

bvecs = load('bvecs'); % should be 3xN

bvals = load('bvals'); % should be 1xN

bvals_b1000=[];

bvecs_b1000=[];

bvals_b0=[];

bvecs_b0=[];

% get b=1000 bvals and bvecs

for j=1:size(bvals,2);

if bvals(1,j)<1500 && bvals(1,j)>500

j-1

bvals_b1000=[bvals_b1000 bvals(:,j)];

bvecs_b1000=[bvecs_b1000 bvecs(:,j)];

end

% get b=0 bvals and bvecs

for j=1:size(bvals,2);

if bvals(1,j)<500

%j-1

bvals_b0=[bvals_b0 bvals(:,j)];

bvecs_b0=[bvecs_b0 bvecs(:,j)];

end

bvals_b1000=[bvals_b0 bvals_b1000];

bvecs_b1000=[bvecs_b0 bvecs_b1000];

dlmwrite('bvals_b1000',bvals_b1000,' ')

dlmwrite('bvecs_b1000',bvecs_b1000,' ')

end

On Thu, Oct 8, 2015 at 11:55 AM, Mark Pinsk <[log in to unmask]> wrote:

Hi fsl,

Thanks so much for 5.0.9, lots of useful improvements! I have a few questions/requests...

bedpostx has a new model (model=3) instead of using a stick kernel to represent a fibre compartment, a “zeppelin” axially symmetric tensor can be used.
Can anyone recommend a good reference to read up on this zeppelin model and how it performs compared to the stick model?

select_dwi_vols allows quick extraction of a certain b-shell from DWI data-
This is great! Could a future release also output a new bvecs file? When shells are interleaved, it's annoying to create a new bvecs file of just a single shell.

eddy will generate a rotated bvecs file.
Awesome, thanks Jesper !!

best,
Mark