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Hi Douglas, I applied a non-rigid registration to my nifti files using another software (IRTK) and then tried to run dt_recon in Freesurfer. Dt_recon is failing during Fitting Tensors and the error message it is displaying is "ERROR: DTIstructFromBFiles(): dimension mismatch" the error message goes on to say that my bvecs file has 99 rows while my bvals file has 11 rows.

I've looked at my bvecs and bvals files: the bvecs has 33 rows and 3 columns, and the bvals has 33 rows and 1 column.

Can you tell me what the problem is? Is there a way to get past this error?

-Hedyeh

Date: Tue, 24 Apr 2018 13:20:20 -0400 From: Douglas Greve dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Non-rigid registration approaches To: freesurfer@nmr.mgh.harvard.edu Message-ID: 52506cd6-286b-21a0-859a-1cda85557bad@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

Sorry, I don' know what to tell you.

On 4/21/18 5:34 PM, Hedyeh Javaheri wrote:

Thanks for your reply Douglas,

I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer?

Thanks

-Hedyeh