Nope, sorry. You can use our dt_recon program to do the tensor fit, but it might not be compatible with higher level FSL routines.

Alina Jurcoane wrote:

Hi,

I have a Siemens DTI dataset which I am converting with mri_convert (freesurfer) from dicom to nifti and then fitting the tensors with FSL.

Since mri_convert outputs my data in Neurological orientation, despite of fsl's warnings about flipping, I have to do fslswapdim and fslorient -swaporient in order to see my data properly in fsl.

The problem is that tensors are fitted wrongly unless one flips the bvecs (outputted by freesurfer) as well.

Is there any simple way to do the whole process dicom->nifti->fit without having to flip data and bvecs? For instance, is there some option to tell mri_convert to output my data AND gradient information in Radiological orientation?

Thanks for the help! Alina

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer