What I was saying was that the structural and diffusion data are already
exactly aligned in the HCP¹s space (which differs from FreeSurfer space by
an exact transform that is already known). There is no need to perform
any further registrations.
On 5/10/18, 7:26 AM, "FSL - FMRIB's Software Library on behalf of Jonathan
Bain" <[log in to unmask] on behalf of [log in to unmask]>
>You're right, the images are aligned to each other. What I meant to write
>was that, for some subjects, the output matrix of the
>ion) was calculated incorrectly. Since I pass this matrix
>(freesurfer2fa.mat) into the probtrackx2 command, the analysis would be
>incorrect if the transform is off.
>In the past, I have found that skull-stripping can help in instances of
>problematic registration. For my previously problematic HCP subjects, I
>found that when I added a skull-stripping step before computing this
>matrix, the freesurfer2fa.mat was now computed correctly.