Hello SPMrs, I am beginner user, my apologies in advance for my simple questions.
I am inspecting motion parameters of my functional scans before the pre-processing.
After realignment estimation, the scans look good within each session (checking translation realignment parameters), but sometimes sub-optimal between sessions (checking the realigment graphs, I see sort of "steps" in some translation parameter lines, for a number of millimeters between the size of 1-2 voxels, clearly starting at the beginning of a new session, e.g the third in the example attached).
I would like then to manually reorient these images between sessions, for the same number of millimeters I read in the realignment graph, using as reference the first image of the first session (the zero).
In Display, I choose the first functional scan of the third session, I entered the numbers, with opposite signs, in right, forward and/or up transformation options (in the case in attachment I put: forward -5 and up -2)
I clicked reorient images..., I choose all the scan of the third and fourth sessions and waited till the program has reorientated all of them.
Does the re-orientation work like this? I am not sure because after that I did my realignment estimate again...but the graph did not change at all.
Should I do the reorientation in a different way?
Or perhaps the reorientation procedure is not appropriate for this purpose?, or it went right but the graph is not not supposed to change.
Final doubt: is the manual matching between sessions necessary before starting automatic pre-processing, and does it improve the quality of the data eventually, or it is unnecessary given the realignment function during the spatial pre-processing?
Thanks a lot for your attention and any help.
Sara
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