Hi Donald,
I am not sure what we mixed up. I did the first level analyses in each
subject showing the expected left-sided frontal lobe activation pattern
in almost each subject (I checked this and it can also be seen in the
first level group results). I used the individual con-images of the
contrast of interest from the first level analyses for the second level
analysis (one con-image per subject) and the pattern disappeared.
If anyone is interested, we could send the con-images and our batch
files.
Thanks,
Kirsten
---------------------------------------------------------
Dr. Kirsten Labudda, Dipl.-Psych.
Krankenhaus Mara
MRT-Abteilung
Tel.: 0521-772 777 61
&
Station für Psychosomatische Epileptologie
Tel.: 0521-772 789 22
---------------------------------------------------------
>>> "MCLAREN, Donald" <[log in to unmask]> 7.11.2012 18:34 >>>
Kirsten,
You are mixing up analysis approaches.
Your first level is combining all subjects using a fixed effects
analysis across subjects. The results do not generalize across the
populations. The DF is extremely high and the variance is the related
to TR-to-TR differences. In general, first level models only contain 1
subject and you use the con_*img at the second level.
The second-level analysis is a test of the mean of the subjects
compared to the variance between-subjects. Its a random-effects
analysis, which means that you can generalize the results to the
entire populations.
As the two analyses are quite different in what they measure and how
to interpret them. It is not surprising to see the differences. Now,
if you see an effect in every subject (1 subject per first level
model) and nothing at the group level, I'd be more concerned.
Hope this helps.
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
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On Wed, Nov 7, 2012 at 12:13 PM, Kirsten Labudda
<[log in to unmask]> wrote:
> Yes, those activations were located within the basal ganglia ... and
it
> does not make a lot of sense (at least if it is the only activation
that
> 'survived'). I also ran these analyses in a larger sample (22
subjects).
> The first versus second level discrepancy also occured. The
> normalization seemed to be ok. Nevertheless, we also applied a
> non-linear normalization, but the 'unusual' results remained. I'll
check
> the amount of movement again.
> I attached some of the results again. I think the first file was to
> large for the mailing list.
> Thanks again,
> Kirsten
>
>
> ---------------------------------------------------------
> Dr. Kirsten Labudda, Dipl.-Psych.
>
> Krankenhaus Mara
>
> MRT-Abteilung
> Tel.: 0521-772 777 61
> &
> Station für Psychosomatische Epileptologie
> Tel.: 0521-772 789 22
> ---------------------------------------------------------
>
>>>> Chris Watson <[log in to unmask]> 7.11.2012
> 17:46 >>>
> Is that bilateral thalamic and caudate activation? Is that something
> that makes sense for your experiment?
> I think what you're seeing *could* be due to only having 9 subjects;
> however, if you see the standard L frontal activation in most/all of
> them, then I don't know what might be causing the discrepancy. Is
there
>
> an especially high amount of motion in these subjects? Does the
> normalization look right?
>
>
> On 11/07/2012 11:46 AM, Kirsten Labudda wrote:
>> Dear Chris,
>> thanks for your quick response. I attached the screenshots of both
>> first and second level analyses versions I conducted (version 1:
> only
>> the activation condition was modelled; version 2: activation and
> rest
>> was modelled on the first level) in the small group. I used the
> movement
>> parameters as regressors in the first level analysis. The second
> level
>> results are thersholded at p<.001 as only very few voxel survived
> the
>> thershold of p<.05 FWE corrected on the second level.
>> Thanks for your help!
>> Kirsten
>>
>> ---------------------------------------------------------
>> Dr. Kirsten Labudda, Dipl.-Psych.
>>
>> Krankenhaus Mara
>>
>> MRT-Abteilung
>> Tel.: 0521-772 777 61
>> &
>> Station für Psychosomatische Epileptologie
>> Tel.: 0521-772 789 22
>> ---------------------------------------------------------
>>
>>>>> Chris Watson<[log in to unmask]>
7.11.2012
>> 16:38>>>
>> Can you post screenshots of your design matrix, the results of 1st
> and
>>
>> 2nd-level analyses, etc?
>>
>> Regarding your design: you only need one regressor, for the task. A
>> contrast of "1" will reflect "task> rest".
>> You also might want to exclude the movement parameters, if your
>> experiment is a block design. Check what the literature says on
that
>> matter.
>>
>>
>> On 11/07/2012 09:46 AM, Kirsten wrote:
>>> Dear fMRI-experts,
>>> we wonder about conflicting results of the first and second level
>> analysis we conducted with our fMRI data. We used a simple blocked
>> verbal fluency task with one activation condition (verbal fluency,
> 10
>> blocks) and a rest condition (also 10 blocks). I wonder, whether we
> did
>> something wrong when using SPM (we used SPM8 and 5 and have the
> problem
>> with both versions). That’s what we did: After preprocessing
>> (realignment, normalization, smoothing), we conducted a first level
>> analysis specifying the verbal fluency blocks as activation
condition
> in
>> each subject (by entering the onset scans of each block and its
> duration
>> in terms of scans) and used the movement parameters as individual
>> regressors. We defined two contrasts (verbal fluency: 1 and rest:
> -1).
>> Is it ok not to model the resting condition separately? We thought
so
> as
>> our design only includes two conditions and with that the vector 1
>> automatically contains the information activation> rest, right?
>> Nevertheless, I also conducted the first level analysis with the
two
>> conditions modeled separately using two T-contrasts then (verbal
>> fluency> rest: 1 -1 and rest>verbal fluency -1 1). Both first
> level
>> procedures lead to very similar results reflecting typical cortical
>> language activations.
>>> I then used the contrast images (the activation condition>rest,
> again
>> of both first level procedures described above) in the second level
>> analysis to run a one-sample t-test with the contrasts: activation>
>> rest: 1 and rest>activation: -1. Surprisingly, the typical cortical
>> language activation from the first level analysis completely
>> disappeared. Instead, only subcortical activation remained (that
was
>> present in the first level analysis, too, but it was much weaker
> than
>> the typical language activation).
>>> We have the problem of very incongruent first and second level
>> results with SPM5 and 8 and within two different patient groups
(one
> was
>> small having 8 subjects only, but the other group includes 22
>> subjects).
>>> Does anybody have an idea why the first and second level results
> are
>> so divergent? Did we simply do something wrong in SPM?
>>> Thanks in advance,
>>> Kirsten
>>>
>>
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