Sara,

The graph is telling you how much it moved the data to make all the
images line up. As such, the jump has already been corrected. It is
quite common to see jumps like this between sessions as subjects might
reposition themselves.

If you are concerned about the alignment between sessions, look at an
image from each run and you will be able to tell if the alignment
worked quite quickly for large jumps noted in the realignment plot.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Jan 29, 2013 at 9:23 AM, Ambrosino de Bruttopilo-3, S.
<[log in to unmask]> wrote:
> 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
> ------------------------------------------------------------------------------
>
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>
> ------------------------------------------------------------------------------
>
> This message may contain confidential information and is intended exclusively
> for the addressee. If you receive this message unintentionally, please do not
> use the contents but notify the sender immediately by return e-mail. University
> Medical Center Utrecht is a legal person by public law and is registered at
> the Chamber of Commerce for Midden-Nederland under no. 30244197.
>
> Please consider the environment before printing this e-mail.