What is the acceptable movement units? What to do if it’s higher than the threshold?
How can you check movement of a particular participant?
How can we make our realignment better? What parameter should we modify?
What is the output of realignment? How do we use it in GLM?
When should you realign to the the first, mean or last image when doing realignment?
Slicetiming correction
Why do we do slicetiming correction?
What does TR mean?
Why do you think slicetiming correction is important particularly for event related designs?
What parameters do we use while doing slice time correction? Check our EPI sequence and in what way we acquire our slices.
What happens in an interleaved slice acquisition? How does it compare to a descending/ascending slice acquisition?
Check what caveats there are out there for interleaved slice acquisitions (spin-history effects)
How long does it take for each slice to be acquired?
What do you think the reference slice parameter pertains to? Which reference slice would be better to use? Why/why not?
What is the output of slicetiming correction?
In our regular EPI protocol, how many slices do we take per TR?
Normalization
Why do we normalize?
What is the MNI template? Why is it called MNI152? How was MNI152 “generated”?
In what situation do you think we may not want to normalize our images?
What is the output of our normalization?
The normalization parameters which we generate from normalization can be used to do subject space analysis and ROI estimation. What kind of parameters can we be using to do this?
Smoothing
Why do we smoothen our data?
When should we not smoothen our data?
How do we smoothen our data? What does the kernel size FWHM correspond to? On what ground do we choose it’s values?
What is the output of smoothened data?
Coregisteration / Segmentation
Why do we do and what do we do in coregisteration?
Why do we do and why do we do tissue segmentation?
How do you check if your data is coregistered properly?