we are using using nipy.SpaceTimeRealigner as a node in our nipype workflow before applying melodic.
Without using the realigner the 9th IC clearly resembles the stimulus induced activity as follows (upper figure).
Whereas, if we do use the SpaceTimeRealigner method, the temporal dependency on the stimulus gets lost and also does not occur in any of the other ICs (lower figure). If we just use the spm.realign method, this does not happen and stimulus reflecting activity is preserved.
This is mouse fMRI, and the slice selection is done axially - meaning that the slices are coronal (not horizontal). this is due to the mouse brain not being bent at 90° in the middle (as e.g. the human brain is).
We should definitely try disabling the time realignment; I was unaware that this can be done by omitting inputs. However, since our mice are well fixed and anesthetized, spatial realignment is of less concern to us than slice timing correction. So we definitely want to be able to do slice timing correction (preferably via a python tool) - it’s spatial realignment which we could forego.
Not least of all, our stimulus evoked activation is quite strong, and spread across much of the cortex. I was afraid, that it might get categorized and filtered out as “motion” - do you know if SpaceTimeRealign does motion correction behind the scenes? We had trouble actually understanding the code.