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Subject:

Re: Head movements and quality of realignment

From:

Paul Mazaika <[log in to unmask]>

Reply-To:

Paul Mazaika <[log in to unmask]>

Date:

Tue, 20 Jan 2009 10:05:46 -0800

Content-Type:

text/plain

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Stephen,

>2. As far as I understand, what I see in spm2.ps is what was really
>corrected during the realignment. Is the any tool to make visual inspection
>to assess whether realignment was good? Something similar to AnalyzeMovie 
of
>SPM99? 

The >>art_movie command in the ArtRepair Toolbox lets the user make a visual review of the effect of realignment. Use it see the data variation in the images before realignment,
and the data variation after realign and reslice. The realigned files must be resliced
for it to work correctly. Incidentally, this script was built using parts from
AnalyzeMovie and spm_movie, with an enhancement to view the variations at greater sensitivity.  

 Paul

 
----- Original Message -----
From: "Stephen J. Fromm" <[log in to unmask]>
To: [log in to unmask]
Sent: Saturday, January 17, 2009 5:29:12 AM GMT -08:00 US/Canada Pacific
Subject: Re: [SPM] Head movements and quality of realignment

On Fri, 16 Jan 2009 22:01:12 +0000, <John> <Gelburg> 
<[log in to unmask]> wrote:

>Hi,
>
>Attached two spm2.ps files with different head movements patterns: slow
>drift in the session and abrupt head movement between sessions. 
>
>A couple of questions:
>1. In general, is movement between sessions preferable than during the
>session and it can be better corrected in realignment procedure?
>Consequently, 2 mm drift during the session is much more harmfully than
>between sessions?

I think displacement (translational and rotational) is more harmful within a 
session than between sessions, for a reason having to do with the statistical 
analysis stage.

In most fMRI experiments, all conditions occur within all sessions.  So we can 
view a contrast as within-session, with the results then _averaged_ across 
sessions.

Contrasts involve subtraction (within a session), and subtraction interacts 
with motion in a "bad" way.  But averaging uses addition, which is in a way 
a "smoothing" operation.

So, for example, if you take two images, one of which is slightly displaced from 
the other, and subtract, you'll pick up things like edges.  On the other hand, if 
you add, you'll kind of blur the image.

_Apart_ from this statistical point, and only looking at the problem of motion 
correction itself, it's not clear to me which is worse.  One difficulty with EPI is 
image distortion:  the distortion (as far as I know) depends on position in the 
field.  So large movements (perhaps even purely rotational) will also modify 
the shape of the brain in the image, which can only be dealt with by "unwarp" 
procedures.  In that sense, more movement is probably worse regardless of 
whether it's between- or within-session.

So I don't think you can say that movement between sessions is easier to 
correct.  Certainly there's nothing in the algorithm in SPM that would make it 
so.  You can only argue as I do above that motion between sessions is less 
harmful to the statistical design.

>2. As far as I understand, what I see in spm2.ps is what was really
>corrected during the realignment. Is the any tool to make visual inspection
>to assess whether realignment was good? Something similar to AnalyzeMovie 
of
>SPM99?

I don't know of any; maybe someone wrote a script.

>Thanks,
>John
>

-- 
Paul K. Mazaika, PhD.
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
Office:  (650)724-6646             Cell:  (650)799-8319

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