Hi Cat - If the gradients were wrong you'd know it, since the tracts would really not look right at all. It doesn't sound like it's a problem.
a.y
On Wed, 30 Oct 2013, Cat Chong wrote:
Dear Experts, I was hoping you could help me with the following problem. Tracula failed when I attempted to use Siemens (Skyra) dicoms as input for the configuration file, so I converted the dicoms to niftii format using dcm2nii. I used the gradient information of the bvec file created by dcm2nii ( after re-assembling it into the appropriate 3 column format) and specified it as the bvec.txt file to run Tracula. All post- processing worked fine and the fiber paths look ‘ok’ as far as I can tell. Here is the conundrum: When I compared the bvec gradients from the dcm2nii conversion to the SIEMENS hardwired protocol, the sign of the ‘z’ direction appears to have been flipped? I am not sure why this happened and whether to choose the “hardwired” Siemens scanner bvecs or the ones created by the niftii conversion. Which ones are correct to use? Very best regards, Catherine