Vish,
On the GE scanner you can select the phase encoding direction, make
sure this is set properly (A/P). In your example you could swap x and
y gradients and get a decent looking color map, but just make sure the
signs are ok if you want to do any kind of tractography.
You could muck with tensor.dat if you want b=0 images sprinkled
through your data although I believe FSL wants all the b=0 images up
front. I don't see any good reason to intersperse them for most
applications however.
Andy
On Mar 18, 2010, at 1:04 PM, Vishwadeep Ahluwalia wrote:
> Hi all,
> I acquired DTI images at a GE-3T using a standard coil as well as an
> 8-channel coil (using ASSET). I then converted the respective dicoms
> into
> nifti using dcm2nii thus producing the respective the nifti files as
> well as
> the bvals and bvecs. dtifit produced the fa and V1 files that were
> different
> for each coil(see attached). The standard coil vectors seem to be in
> the
> correct orientation but the multichannel coil vectors seem
> interchanged
> between x and y ( red and green). The bvecs were the same for the
> two. Upon
> looking at the dicom headers i found that the standard coil data was
> acquired with 'In-plane phase encoding direction' as COL (y
> direction i
> guess) and 'In-plane phase encoding direction' as ROW ( x direction)
> which
> might explain the flip. So should i correct for this by simply
> exchanging
> the x and y vectors in bvecs?
>
> I also acquired 4 b0 volumes. but i found that all 4 are acquired at
> the
> start of the scan. Doesnt this defeat the purpose of acquiring
> multiple b0?
> I thought these have to be interleaved between different gradient
> directions. How can i do this on a GE Discovery -750 3T magnet?
> Also, i would appreciate any advice on using multichannel coil for
> dti. As
> in, is it better than standard coil for SNR, distortion etc. Thanks!
> -Vish
>
> <multicoil1.jpg><standardcoil1.jpg>
Andrew Alexander, Ph.D.
Waisman Laboratory for Brain Imaging
Departments of Medical Physics and Psychiatry
(608)265-8233
Waisman Center
1500 Highland Ave
Madison, WI 53705
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