I haven't used SPM5 much at the single subject level.
I can't find anything about grand mean scaling in the interface. The
code (in spm_fmri_spm_ui.m) makes it look like it's done automatically
if you don't do global normalization (meaning "Global normalization"
equals "none", not "scaling").
Stephen J. Fromm, PhD
Contractor, NIMH/MAP
(301) 451-9265
-----Original Message-----
From: Julia Weiler [mailto:[log in to unmask]]
Sent: Monday, May 19, 2008 10:40 AM
To: Fromm, Stephen (NIH/NIMH) [C]; [log in to unmask]
Subject: Re: [SPM] comparability of data from different scanning
sessions
Thanks for the fast response.
I am using SPM5.
Julia
Fromm, Stephen (NIH/NIMH) [C] schrieb:
>
> It's done at the first level (that is, subject level).
>
> What version of SPM are you using?
>
> Stephen J. Fromm, PhD
> Contractor, NIMH/MAP
> (301) 451-9265
>
>
------------------------------------------------------------------------
>
> *From:* Julia Weiler [mailto:[log in to unmask]]
> *Sent:* Monday, May 19, 2008 10:35 AM
> *To:* [log in to unmask]
> *Cc:* Fromm, Stephen (NIH/NIMH) [C]
> *Subject:* Re: [SPM] comparability of data from different scanning
> sessions
>
> Dear SPMers,
>
> I previously posted a message regarding the analysis of fMRI data from
> different scanning days.
> I received the advice to perform grand mean scaling in order to
> normalize my data.
> Now, I would like to ask for some help regarding how to perform this
> analysis:
>
> Do I have to specifiy grand mean scaling on the 1st or 2nd level of
> the analysis?
> And, if I have to do it on the first level, do I have to use a PET
> model for this operation?
> I could not find an option for grand mean scaling on the first level
> of the fMRI analysis
> (or is it the same as global normalization)?
>
> Thank you very much in advance
>
> Julia
>
>
>
> Fromm, Stephen (NIH/NIMH) [C] schrieb:
>
> There are various forms of intensity normalization.
>
> Grand mean scaling is the "weakest" form: you divide each voxel by
the
> average over "space" and "time", where "space" is "all intracerebral
> voxels" (based on SPM's criteria for what's in vs out of brain) and
> "time" is "all timepoints (volumes) in a given run/session". (I like
to
> call it a "run"; SPM usually calls it a session.)
>
> Since grand mean scaling is "weak," it would be difficult to argue it
> does any harm. And it can do a lot of good: if one run is
arbitrarily
> 7% (say) higher in signal, GMS will take that into account.
>
> A "stronger" form of intensity normalization would be to divide each
> voxel by the average over that single voxel over the entire run. (So
> "space" = "that particular voxel only", and "time" = "that run"; time
is
> the same as in GMS.)
>
> It's debatable whether you should do GMS or the strong "voxel-wise"
> normalization, but you should certainly do GMS. (GMS is provided for
in
> SPM; voxelwise is not hard to do but isn't directly an option in SPM.)
>
> Best,
>
> Stephen J. Fromm, PhD
> Contractor, NIMH/MAP
> (301) 451-9265
>
>
>
> -----Original Message-----
> From: Julia Weiler [mailto:[log in to unmask]]
> Sent: Wednesday, May 14, 2008 8:39 AM
> To: Fromm, Stephen (NIH/NIMH) [C]; [log in to unmask]
<mailto:[log in to unmask]>
> Subject: Re: [SPM] comparability of data from different scanning
> sessions
>
> We did not perform grand mean scaling so far.
> Is it common to do this, if one has data from different scanning days?
>
> Julia
>
>
> Stephen J. Fromm schrieb:
>
>> On Tue, 13 May 2008 09:12:55 +0200, Julia Weiler
<[log in to unmask]> <mailto:[log in to unmask]>
>>
>
>
>> wrote:
>>
>>
>>
>>> Dear SPM experts,
>>>
>>> I am a new user of fMRI and are experiencing some unclarities
>>>
> concerning
>
>>> my data interpretation.
>>> Our task required scanning the same subjects twice on two different
>>>
> days
>
>>> using the same task.
>>> We conducted three conditions (A,B,C) on the first day and one
>>>
> condition
>
>>> (A2) on the second day.
>>> A and A2 were basically the same. The scanner and scanning
parameters
>>> were the same for the two days.
>>>
>>> When extracting the time courses using MarsBaR, we experience the
>>> following strange phenomenon:
>>>
>>> Conditions A,B,and C of the first day usually show similar time
>>>
> courses.
>
>>> However, compared to these
>>> conditions, condition A2 stays always close to zero.
>>>
>>> Hence, significant activations in a contrast A2 > B for instance,
>>>
> seem
>
>>> to be due to deactivation in B
>>> rather than activation in A2. For the reverse contrast, B>A2,
>>>
> however,
>
>>> there seems to be activation
>>> in B and no signal changes in A2.
>>>
>>> This is the same for a large number of ROIs. The time course for the
>>> condition of the second day is
>>> always close to zero with respect to the other conditions (although
>>> condition A2 of the second day
>>> was identical to condition A of the first day).
>>>
>>> Is it necessary to somehow normalize the data if I want to compare
>>> sessions acquired on different days?
>>> Or could I be making any other mistake?
>>>
>>>
>> Did you perform grand mean scaling?
>>
>>
>>
>>> Any suggestions would be very much appreciated.
>>>
>>> Regards
>>> Julia
>>>
>>> --
>>> Julia Weiler
>>>
>>> Ruhr-University Bochum
>>> Inst. of Cognitive Neuroscience
>>> Department of Neuropsychology
>>> GAFO 05/606
>>> Phone: +49-234-3223574
>>> Fax: +49-234-3214622
>>>
>>>
>
========================================================================
> =
>
>>>
>>>
>
>
>
>
>
> --
> Julia Weiler
>
> Ruhr-University Bochum
> Inst. of Cognitive Neuroscience
> Department of Neuropsychology
> GAFO 05/606
> Phone: +49-234-3223574
> Fax: +49-234-3214622
--
Julia Weiler
Ruhr-University Bochum
Inst. of Cognitive Neuroscience
Department of Neuropsychology
GAFO 05/606
Phone: +49-234-3223574
Fax: +49-234-3214622
|