Register FA maps onto freesurfer conformed space


I have a question about registering DTI maps(10210272, 2mm2mm2mm) onto FreeSurfer conformed space(256256256, 1mm1mm1mm), so what i have done was:

  1. register t1 on the umsample b0 image use flirt rigid registration, get the deformation matrix
  2. apply the registration matrix for MD and AD, RD, FA maps with the inversed deformation matrix from step 1 to the FreeSurfer space
  3. resample the registered FA map into the same size in Freesurfer space (256256256, 1mm1mm1mm)

I did try resampling the FA map before and after registration use mri_convert, but the results do not look well, even the resampling process changes also the space.

Any one have some suggestions?


Have you tried the bbregister command from Freesurfer’s package?
If teh EPI signal is good enough, it’s boundary-based registration provides nice results. After computing the registration matrix, with a simple mri_vol2vol, you can have your MD, FA, etc to Freesurfer 256³ space.

Victor M.

Hi, thanks for your advice, I tried that and it works, but I still have a question, why people use FA to do WM analysis, but not normally do GM analysis based on the anatomical MRI segmentation? Is that because the partial volume fraction, the different resolution between T1 and dMRI??

It is due to the microstructure organization. WM has a more directional organization of neurons (tract), and consequently, FA metric will be more sensitive to subtle changes. However, cortical regions (GM) is way more isotropic (no specific organization). Mean diffusivity provides an idea of “how freely” the water moves depending on different physipathological process/structures. For example, neural death will allow the water to move more freely, and you will capture higher values of mean diffusivity. On the other hand, inflammatory processes (such in Creutzfeldt-Jacob disease) will result in “less free movement of water” and lower MD values.

We will publish soon a paper assessing MD in Alzheimer’s Disease, if you are interested, using a similar pipeline as the described above. Also, you can read this paper for more info.

Victor Montal

thanks for your reply, look forward for your new published paper, I did my pipeline by using flirt to do the registration and the results look good by visual checking, I am curious how you can avoid the partial volume effect. Let’s say if you use ROI-based approach, for the subcortical structure, it is rather big, maybe we can just make an erosion, but for the cortex, it is quite thin, how would you avoid the CSF contamination even the alignment is quite good?

Look forward to your reply