Using FSL - Registration
Before any multi-session or multi-subject analyses can be carried out, the different sessions need to be registered to each other. This is made easy with FEAT, by saving the appropriate transformations inside the FEAT directories; the transformations are then applied when group statistics is carried out, to tranform any relevant statistic images into the common space. By doing this (saving the relevant registration transformations and only applying them to the stats images later) a lot of disk space is saved.
Registration inside FEAT uses FLIRT (FMRIB's Linear Image Registration Tool). This is a very robust affine registration program which can register similar type images (intra-modal) or different types (inter-modal).
Typically, registration in FEAT is a two-stage process. First an example FMRI low resolution image is registered to an example high resolution image (often the same subject's T1-weighted structural). The transformation for this is saved into the FEAT directory. Then the high res image is registered to a standard image (normally a T1-weighted image in standard space, such as the MNI 152 average image). This transformation, also, is saved. Finally, the two transformations are combined into a third, which will take the low resolution FMRI images (and the statistic images derived from the first-level analyses) straight into standard space, when applied later, during group analysis.
You can carry out registration for each first-level analysis at the same time as the original analysis, or get FEAT to "register" a pre-existing FEAT directory, at a later time. In the latter case, change the Full analysis to Registration only.
The Initial structural image is the high resolution structural image which the low resolution functional data will be registered to, and this in turn will be registered to the main highres image. It only makes sense to have this initial highres image if a main highres image is also specified and used in the registration.
One example of an initial highres structural image might be a medium-quality structural scan taken during a day's scanning, if a higher-quality image has been previously taken for the subject. A second example might be a full-brain image with the same MR sequence as the functional data, useful if the actual functional data is only partial-brain. It is strongly recommended that this image have non-brain structures already removed, for example by using BET.
If the field-of-view of the functional data (in any direction) is less than 120mm, then the registration of the functional data will by default have a reduced degree-of-freedom, for registration stability.
If you are attempting to register partial field-of-view functional data to a whole-brain image then 3 DOF is recommended - in this case only translations are allowed.
If the orientation of any image is different from any other image it may be necessary to change the search to Full search.
The Main structural image is is the main high resolution structural image which the low resolution functional data will be registered to (optionally via the initial structural image), and this in turn will be registered to the standard brain. It is strongly recommended that this image have non-brain structures already removed, for example by using BET.
Standard space refers to the standard (reference) image; it should be an image already in Talairach space, ideally with the non-brain structures already removed.