Hi, all~
I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and the log, but found nothing, except copy and Eddy-current "correction".
ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is read from the DICOM header via nibabel. But FSL requires LAS. I thinks trac-all have done the transposition on the bvecs somewhere. What orientation of bvecs does trac-all need when run with .nii files?
Thanks!
Xiangzhen
2012-02-03
When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi, all~ I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and the log, but found nothing, except copy and Eddy-current "correction". ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is read from the DICOM header via nibabel. But FSL requires LAS. I thinks trac-all have done the transposition on the bvecs somewhere. What orientation of bvecs does trac-all need when run with .nii files? Thanks! Xiangzhen 2012-02-03
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Xiangzhen Kong