Shifted or Rotated Functional Images

Overview:

Sometimes functional data will be "shifted" (misaligned) or "rotated" (by 90 deg) with respect to the anatomical images. Thre are two ways that you can check for this in mrLoadRet. First, view the tSeries movie with anatomies (from the View menu). Second, compute the mean map (from the Analysis menu) and view it overlaid (with appropriate slider settings) superimposed on the inplane anatomies.

This misregistration happens when the scanner's reference point for the center of an image is inconsistent between anatomical and functional scans. Forgetting to select Fallback before one set of scans can cause this (Fallback should always be selected for both the inplanes and the functionals).  Finally, data-shifts can also occur when the subject moves their head between scans. If your data-shift is the result of Fallback registration, you have a simple and exact correction to make. If head-movements occurred, correction can be approximated, but won't be exact. If data is shifted by Fallback misregistration, the amount of shift corresponds to the difference between the location of the center of the bore and the location of the sagittal slice used to pick the inplanes (as on the screen save). Since this difference is the value on the upper-right corner of the screen save (eg, 'R2.5'), it is easy to arrive at an exact solution for all scans. If you suspect that the shift is due to a between-scan head movement, you can try to use the motion compensation utilities in mrLoadRet (Analysis menu).

The image rotation happens because of a bug in the reconstruction code. The rotation is always 90 degrees so it is easy to fix.

How to un-shift or un-rotate functional data:

These steps assume that you already have a P*.mag file (from Gary's autorecon). If you don't, then you will first have to compute it from the raw Pfile before you can proceed.

1) Estimate the amount of shift. If you suspect Fallback misregistration, the size of shift should be the value in the upper-left corner of the screen save (e.g., 'L10.0').

2) run matlab

3) Run the GetRecon: GetRecon (rawDir, compFlag, rotFlag, shifts) where