[Camino-users] flirt seeds the fa.nii's dimension but disproportionate in view

[Philip A Cook]

Hi,

The seed image may be of higher or lower resolution than the FA, but it should be physically aligned. For example, in the attached image, the brain on the left is sampled at 1mm, the brain on the right at 2mm, but when I load them both in ITK SNAP, the physical coordinates (crosshairs) are aligned anatomically.



You can certainly reslice the seed image to be the same dimensions as your FA image. Flirt ought to do this, though there are ways to make it behave differently. (eg, -noresample).

Anyway, track will initiate N streamlines (-iterations N) from the center of each voxel with a positive, non-zero label. For it to be successful, you need to ensure that your seed and diffusion space are aligned.


On Jul 13, 2015, at 2:17 PM, zeno Zeng <zeno3175 at gmail.com> wrote:

> Hi all, 
> 
> I an new to Camino Toolbox. I run probabilistic tractography with "track" on a seed region. Since I generated my seeds through FSL,  they have different dimensions with the fa.nii and md.nii. So I "flirt" the seeds to fit the dimensions of the fa.nii and md.nii. 
>         Though the "track" function can be run(not yet finished), but visually the seeds are disproportionate, way bigger than the fa.nii (whole brain image) in fslview. 
>          Is there a way that I can have seeds and fa.nii in the same dimensions and proportionate visually as well? I was thinking if they can be both registered to a brain model and then reslice (flirt) and then run the "track". 
> 
> Thank you ! 
> Jacqui 
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