On Jul 11, 2013, at 4:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu>

wrote:

you can run bbregister using the b=0 image as input. The final cost
function value should beless than .9, if it is more than that then it
probably means you have an LR flip.

doug

On 07/11/2013 03:52 PM, Barron, Daniel S wrote:

Dear Freesurfers,

I am trying to perform probabilistic tractography (FSL Probtrackx) between seed and target VOIs made with Freesurfer's recon-all (T1) and dt_recon (DW) pipelines.

I have the original T1 DICOMs, however, I only have the DW NIFTI image volumes. I do not know how the DW DICOMS were converted to NIFTI and am worried about L-R flipping.

Within Mango, I have found the T1 images converted with mri_convert are (X+,Y-,Z+). The DW NIFTI is (Y-,Z-,X-). mri_info gives me a lot of information that, unfortunately, I do not entirely understand.

Can you recommend a way for me to verify consistent orientation in both my T1 and DW images? Thank you!

Cheers,
Daniel

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Douglas N. Greve, Ph.D.
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