When you run McFlirt in Feat gui, you get 3 graphs telling about displacements. Are these the displacements found BEFORE motion correction has been applied, or after?
Various web sources suggest you can use the 3rd graph (“Estimated mean displacements”) as a rule-of-thumb guide for whether movement is acceptable or not. The rule most often says, if the greatest movement is < 1-2 mm (for a 3x3 voxel size), then the movement in the scan is ok. However if the graph shows the data before MC is applied, you can't really apply this rule... because you don't know what the final (corrected) displacements are.
Also is there a way to get these graphs when you run mcflirt from the command line? I don't see an option for this.
Thanks for your help...
-Christina Fales
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