bbregister should work well for this application. If it runs into a problem, it usually means that the initialization failed. Did you collect the anatomical in the same session as the functional? If so, try using --init-header. If not, did you collect any whole-brain data set in addition to your 12-slice slab? If so, try passing that volume as an intermediate (--int).
doug
On 12/16/10 3:35 PM, Bruce Fischl wrote:
Hi Joakim
FYI Doug is on vacation and might be a bit slow in answering.
cheers Bruce
On Wed, 15 Dec 2010, Joakim Vinberg wrote:
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
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