Data preprocessing

For each piece of software used, give the version number (or, if no version number is available, date of last application of updates).
If any subjects required different processing operations or settings in the analysis, those differences should be specified explicitly.

Pre-processing: General

Slice-timing correction
- Reference slice and type of interpolation used (e.g. "Slice timing correction to the first slice as performed, using SPM5's Fourier phase shift interpolation")

Motion correction
- Reference scan, image similarity metric, type of interpolation used, degrees-of-freedom (if not rigid body) and, ideally, optimization method (e.g. "Head motion corrected with FSL's MCFLIRT by maximizing the correlation ratio between *** and *** the middle volume, using linear interpolation."
- Motion-susceptibility correction used

Intersubject registration

Intersubject registration method used
- Illustration of the voxels present in all subjects ("mask image") can be helpful, particularly for restricted fields of view (to illustrate overlap of slices across all subjects). Better still would be an indication of average BOLD sensitivity within each voxel in the mask.
Transformation model and optimization
- Transformation model (linear/affine, nonlinear), type of any non-linear transformations (polynomial, Discrete Cosine Basis), number of parameters (e.g. 12 parameter Affine, 3x2x3 DCT basis, regularization, image-similarity metric, and interpolation method.
Object Image information. (Image used to determine transformation to atlas)
- Anatomical MRI? Image properites (see above).
  - co-planar with functional acquisition?
- Functional acquisition co-registered to anatomical? if so, how?
  - Segmented grey image?
  - Functional image (single or mean)
Atlas/target information
- Brain image template space, name, modality and resolution.
  - (E.g. "FSL's MNI Avg152, T1 2x2x2mm"; "SPM2's MNI Gray Matter template 2x2x2mm")
- Coordinate space?
  - Typically MNI, Talairach, or MNI converted to Talairach
  - If MNI converted to Talairach, what method? E.g. Brett's mni2tal?
  - How were anatomical locations (e.g. gyral anatomy, Brodmann areas) determined? (e.g. paper atlas, Talairach Daemon, manual inspection of individuals' anatomy, etc.)

Smoothing

Size and type of smoothing kernel (provide justification for size; e.g. for a group study, "12 mm FHWM Gaussian smoothing applied to ameliorate differences in intersubject localization"; for single subject fMRI "6mm FWHM Gaussian smoothing used to reduce noise".