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Hi Sara

You can only use transformations estimated using FLIRT. I am afraid bbregister uses different conventions for storing the transformation. You should either find out how to get a bbregister transform into a FLIRT-like format, or use FLIRT with BBR cost-function to estimate your transformation.

Cheers
Saad

On 2 Aug 2017, at 20:44, Sims, Sara A <[log in to unmask]<mailto:[log in to unmask]>> wrote:

Hello,

I am having an issue with and error when using the probtrackx gui. I have selected single mask; selected a .nii label in structural space for seed image; checked seed space is not in diffusion; selected the output .mat of the transform from diff to structural using bbregister; checked surface; selected freesurfer mesh convention; surface register image is the T1 from freesurfer reconall. See attached image of the gui and error. I selected an empty output directory and hit go.
I then get the error: “terminate called after throwing an instance of NEWMAT::NotSquareException”.
Where did I go wrong?
<image001.png>

Thanks,
Sara