Hi FSLers--
Thanks to Jesper and others for input on my registration woes. Removing the neck from the MPRAGE was one of several big problems in registering the High Res image to the Standard. However, I'm still having significant problems with registration. I do have a fair amount of ghosting in my images, because Fat Sat was turned off in order to have a sequence with TR=2000. At least I was told that Fat Sat had to be turned off for the sequence to be this fast.
I've attached one picture which highlights my problem. It appears as though the EPI image is highly distorted in the right hemisphere (left side of display) and my thought is that this is driving all of my registration problems. I ran BET ("apply to 4D") with the default fractional intensity threshold of 0.5 to my 4D data and this removed almost all of the ghosting except for the two most superior slices and the distortion was reduced but still a problem. My other pre-processing steps include:
MCFLIRT
Slicetiming *I've taken this out in case I made a mistake in my slicetiming file
Smooth FWHM
Registration - Main structural image - Linear: Normal search with 6 DOF
Registration - Standard Space - Linear+Nonlinear with MNI152_T1_2mm_brain Warp Res=10mm
The participant is a typically developing 12-yr-old who had a max translation movement of 0.5mm. I ran this data through SPM5 and from what I can see by eye using check reg, the registration looks acceptable and my activation map is in line with predictions for my set-shifting task. What am I missing?
Thanks for the help!
Ben
