single slice alignment

Hello experts!

I am reaching out for advice on aligning a single slice to the T1 structural scan. 3dvolreg seems to do an ok job, but it is a little off. I am hoping that there is a script or some other way to align them properly.

Any help on the matter would be very much appreciated.


Zac Fernandez

Hi, Zac-

Does your single slice have similar contrast to the T1w volume (I assume it does, if 3dvolreg did OK)? Also, is the slice starting off in approximately the right place (again, I assume it does if 3dvolreg did a good job)?

Assuming “yes” replies to both of the above, you could try this linear affine (12 DOF, instead of 3dvolreg’s rigid body 6 DOF) alignment, using probably a better cost function (LPA, instead of 3dvolreg’s LS):

3dAllineate \
  -twopass \
  -lpa  \
  -source SLICE_DSET \
  -base FULLVOL_DSET \
  -prefix OUTPUT_SLICE \
  -1Dmatrix_save slice_to_vol.aff12.1D

But whether the command above works well depends heavily on the initial questions.