Hi Gabor - If you provide the DWI dicoms directly, tracula uses
mri_convert to convert them to nifti, and mri_convert doesn't read
directions from the header, it looks them up from:
$FREESURFER_HOME/diffusion/mgh-dti-seqpack/
This should be fine assuming you use the same standard Siemens diffusion
protocol that we use at MGH. If you're using anything different than that
(including if you concatenate two DWI series into one), then you should
set bvecfile, bvalfile, nb0. For more info see:
http://www.freesurfer.net/fswiki/dmrirc
If you have doubts about your bvecs is you can check the primary
eigenvectors from dtifit (dmri/dtifit_V1.nii.gz) to make sure they're
pointing the way you'd expect.
Hope this helps,
a.y
On Sat, 31 Mar 2012, Gabor Perlaki wrote:
Dear Freesurfers,
I have DTI images acquired on a Siemens 3T TIM Trio (software version
VB17A).
1, Is TRACULA able to extract the correct b-values and b-vectors from the
DICOM headers of Siemens IMA files or do I need to specify them?
2, I'm not sure whether the gradient directions are stored in the image- or
in the scanner coordinate system in the headers of Siemens IMA files. Does
anybody have any experience with this version of Syngo software (VB17A)?
Does TRACULA need the b-vecs in the image or in the scanner coordinate
system? Is it able to reorient the bvecs if they are stored in the wrong
coordinate system in the header?
3, My DTI protocol (30 diffusion weighted directions and 1 b0) was repeated
twice (in separate series, the second right after the first one, same
orientation). Because I'd like to correct for eddy current and movement I
don't want to average them on the scanner. Is it possible to put the 62
volume (30+30 diffusion weighted directions and 2 b0) into the same TRACULA
evaluation in dicom format or do I need to convert them into a single niftii
file?
Thanks a lot,
Gabor
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