I would like to ask for your guidance regarding two types of manual image adjustments prior to running fMRIPrep:
- Set origin (translation only) – Using SPM’s “Display” function, I adjust only the Right, Forward, Up values
→ unify the origin across images. - AC-PC alignment (rotation) – Again using SPM’s “Display” function, I adjust pitch, yaw, and roll
→ align the brain along the AC-PC line.
The first approach (set origin) seems more conservative, whereas the second (AC-PC alignment) involves a more substantial transformation. I believe the origin adjustment is generally necessary, but I am unsure whether the rotation-based AC-PC alignment is appropriate, especially if fMRIPrep already performs its own alignment internally.
Therefore, I have the following questions:
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Is it acceptable to perform AC-PC alignment (rotation) before running fMRIPrep, or could it potentially interfere with internal processing steps?
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Does fMRIPrep already include an AC-PC alignment step as part of its preprocessing pipeline? In this case, I would like to know whether this includes both setting the origin (translation) and AC-PC alignment (rotation).
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Would you recommend applying only set origin (translation) before preprocessing, or is AC-PC alignment (rotation) also advised?
Thank you very much for your help.