I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. 

I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.nii file from the recon-all output. Now I need to register the files in the orig.nii space back onto the T1 MRI that is in native space. 

I have tried using  mri_vol2vol to get the files in the orig.nii (recon-all) space into the T1 native space without using a registration file (I used --regheader) and now the registration matrix of my file is the same as the native space, but when I use rview to visualize the registration there are flaws. I've also tried this co-registration using tkregister2 to create a registration file called register.native.dat, and then used mri_vol2vol with register.native.dat; and the results were the same as when I used mri_vol2vol with --regheader.

Is there a tool to do actual manual registration in Freesurfer? Using tkregister2 I cannot perform localized changes; and the global changes it is capable of do not improve on the coregistration.

Here is a breakdown of what I have done: 

subject in Native space to Freesurfer conformed space using recon-all, output: orig.nii 

subject in Native space to other Freesurfer space using dt_recon, output: lowb.nii and register.dat

From the other Freesufer space to Freesurfer conformed space using register.dat, output: lowb2orig.nii

attempting to convert from Freesurfer conformed space to Native space: 

                  using mri_vol2vol and --regheader --> poor registration 

                  using tkregister2 to make register.native.dat, then mri_vol2vol and         register.native.dat --> poor registration

I am running Freesurfer version 6 on Windows.