Hi Brian,
Have you checked the eddy_corrected images before running any further processing? Have you used eddy_correct with the default settings?
I am not sure if that's causing the problem, but notice that by default eddy_correct attempts an affine registration to the 1st volume. Depending on the noise levels and diffusion contrast, this can be a bad choice.
In your case you need to indicate that 61 is your b0 volume by running:
eddy_correct input output 61.
Hope this helps
Stam
On 12 Feb 2013, at 18:16, Brian Stirling wrote:
> Dear FSL experts,
>
> I ran default BedpostX on HARDI images (vols 0-60 have b=1000, vol 61 is b=0 on Philips) on images that had eddy_correct run on them and without. The eddy_correct images seem to produce false directions as seen with the dyads files and as later seen with probtrackx (e.g. an amygdala seed doesn't project anywhere out of close vicinity and voxel coordinates at the corpus callosum seed don't project anywhere either). The non eddy_corrected images seem to work fine. Am I supposed to use eddy_correct images as my data.nii.gz files? The same occurs for a subject of good and bad image quality.
>
> Thank you,
>
> Brian
>
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