[Freesurfer] Alignment of non whole-brain functional slabs

Hi everybody,

I am working towards multi-modal integration of BOLD data. For some of my data, the entire brain was not recorded (in this case, I have 12 slices covering the superior half of the brain). I have been working to align this data using bbregister and have had very inconsistent results: in 1 subject it worked great; in another 6, the alignment failed (resulting in an alignment that is sometimes close, and sometimes way off).

I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I have used this method successfully with a number of other sessions so far (with functional slabs that do cover the entire brain) with outstanding results.

Is this troublesome for bbregister, or is there potentially something I'm doing incorrectly?

Thanks in advance! If I'm repeating well-worn topics, I apologize, I couldn't find anything following a search through the archives.

Joakim