Try using bbregister to register the freesurfer anatomical to the low b in the native diffusion space, then use mri_vol2vol or mri_label2vol to map the ribbon to the native diffusion space.

doug

Theodor R?ber wrote:

Dear Freesurfers,

I am trying to transform a Freesurfer-generated white matter mask (ribbon) to FSL diffusion space in order to use it as a stop-mask in fibertracking. I have tried to coregister and reslice it to the normalized dti_FA with SPM and I also tried to transform it with FSL-FLIRT and FSL-FNIRT as described on http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html. Unfortunately, neither approach yielded satisfying results. What steps would you recommend to turn the Freesurfer output into a FSL-FDT compatible white matter mask?

Thank you very much in advance. Your help will be greatly appreciated.

Best,

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