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fMRI data preprocessing


Normalisation refers to bringing your data into a standard template space to allow group-level statistics.

Why normalise my data?

Normalisation is an essential step in neuroimaging analysis that allows group-level analyses. When neuroimaging data is normalised it means it has been transformed to fit into a standard template space. While many different templates exist, the most commonly used one is MNI152.

For a thorough overview of issues related to normalisation, see the SPM book:

Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2006). Statistical parametric mapping: The analysis of functional brain images.

And other readings:

Ashburner, J. and Firston, K.J. (2005) Unified segmentation.

  1. From the SPM menu panel, select Normalise (Write). You will see a pop-up window appear looking like this:

  2. Select Data New: Subject.

  3. Select Deformation field.
  4. In the pop-up window, use the left-hand panel to navigate to sub-01/anat/.
  5. From the right-hand panel, select the deformation field generated during coregistration - y_sub-01_T1w.nii and press Done.
  6. Select Images to write.
  7. In the pop-up window, navigate to sub-01/func/.
  8. From the right-hand panel, select the realigned and slice time corrected data - arsub-01_task-auditory.nii. Use the box underneath the Filter button to show a 4D file by typing in NaN and pressing Enter. You can do this in combination with filtering for files starting with ar by typing in ^ar.* in the Filter box and pressing Enter.
  9. Optional: Under Writing options, change Voxel sizes form [2 2 2] to [3 3 3]. This will write images at a resolution closer to that at which they were acquired.
  10. Save this batch for future reference - File Save batch and name it, e.g. normalisation_batch.mat.
  11. Run your batch by pressing .

SPM will now write spatially normalised files to the functional data directory, i.e. sub-01/func/. These files have the prefix w.

Video walk-through