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Subject:

Re: Πρ: Απ: [SPM] Factorial design

From:

"Flandin, Guillaume" <[log in to unmask]>

Reply-To:

Flandin, Guillaume

Date:

Fri, 4 Jan 2019 17:25:31 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (138 lines)

Dear Eugenia,

I find it more natural to compare averages so I would use [1 1 1 1 -1 -1
-1 -1]/4 for subjects having four sessions and [1 1 1 -1 -1 -1]/3 for
the subject having only three sessions.
If you already have used [1 1 1 1 -1 -1 -1 -1] for your subjects with
four sessions then, yes, you could use [1 1 1 -1 -1 -1]*4/3 for the
subject with three sessions.

Best regards,
Guillaume.


On 03/01/2019 15:18, eugenia flipakopoulou wrote:
> 
> ------------------------------------------------------------------------
> *Από:* eugenia flipakopoulou <[log in to unmask]>
> *Στάλθηκε:* Πέμπτη, 20 Δεκεμβρίου 2018 10:06 μμ
> *Προς:* Flandin, Guillaume; [log in to unmask]
> *Θέμα:* Απ: Απ: [SPM] Factorial design
>  
> Thank you for your reply.How can I include subjects with less sessions
> in my group analysis?Should all sujects have equal number of sessions or
> do I have to transform the contrasts I define for this person?If for
> example all subjects have 4 sessions and one 3 for this person how I
> change the con image[ 1 1 1 -1 -1 -1] for this person?Do I have to
> multiply with 3/4 for this person?Thank you in advance!
> ------------------------------------------------------------------------
> *Από:* Flandin, Guillaume <[log in to unmask]>
> *Στάλθηκε:* Δευτέρα, 17 Δεκεμβρίου 2018 5:33 μμ
> *Προς:* eugenia flipakopoulou; [log in to unmask]
> *Θέμα:* Re: Απ: [SPM] Factorial design
>  
> Dear Eugenia,
> 
> You should double check what each of the automatically generated
> contrast image corresponds to (by looking at them in the contrast
> manager). Given your next question, I would actually recommend you
> specify the t-contrasts manually at the first level so that they
> correspond to the approach describe in the link of my previous email.
> 
> Concerning your second question, have a look at slide 12 of this
> presentation:
> 
> https://www.fil.ion.ucl.ac.uk/spm/course/slides18-oct/03_Contrasts_and_Inference.pptx
> 
> Best regards,
> Guillaume.
> 
> 
> On 16/12/2018 11:10, eugenia flipakopoulou wrote:
>> Thank you very much !There also some con images that are created
>> automatically after first level specification for factorial and i assume
>> they correspond to the 8 con images i need for a 3x 3 anova .So I used
>> these con images in the second level and performed f tests in the second
>> level.
>> 
>> Another question is that one of my persons has fewer sessions and this
>> is a problem for the second level.How can I include this person easily?I
>> have already  his con images from the automatic procedure of the first
>> level.Do i have to create the con images from that person manually
>> including the number of the sessions?I give you an example of a contrast
>> for that person( 9 conditions, 3 sessions instead of 4 which is the
>> number of sessions for all people):
>> 
>> c=1 1 1 -1 -1 -1 0 0 0
>> ------------------------------------------------------------------------
>> *Από:* Flandin, Guillaume <[log in to unmask]>
>> *Στάλθηκε:* Δευτέρα, 10 Δεκεμβρίου 2018 1:41 μμ
>> *Προς:* eugenia flipakopoulou; [log in to unmask]
>> *Θέμα:* Re: [SPM] Factorial design
>>  
>> Dear Eugenia,
>> 
>> Have a look at this other post that was also concerning a 3x3 factorial
>> design within subject:
>>   https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;1fc74dbb.1812
>> I would recommend to use contrasts on the regressors corresponding to
>> the canonical HRF only (ie use zero weights on time and dispersion
>> partial derivatives). The summary statistics images to bring to the
>> second level are the contrast images (i.e. con_*.nii), not the
>> statistical images (spmT/spmF).
>> 
>> Best regards,
>> Guillaume.
>> 
>> 
>> On 09/12/2018 12:11, eugenia flipakopoulou wrote:
>>> Dear experts,
>>> 
>>> I am running an event related fMRI model consisting of 11 people with 4
>>> sessions each.My statistical model is a 3x3 ANOVA with two factors
>>> consisting of 3 conditions for each factor.Hence, there are 9
>>> conditions( from the combination of the two factors) for each session.I
>>> am particularly interested in the second level analysis and I have some
>>> questions considering the ideal design.
>>> -First of all, in the first level  I used the HF canonical function with
>>> both  derivatives resulting in more betas.Should i prefer the
>>> derivatives or the simple canoonical function is ok?
>>> -In the first level analysis  I specify 9 conditions separately for each
>>> one of the 4 sessions.After I have defined a factorial design then the
>>> SPM automatically creates in the contrast manager the two main effects
>>> and the interaction.For each person a design matrix is created with 4
>>> sessions together ,136 betas ,31 contast images ,4 ess con ,4 spmF
>>> images and 31 spmT images.My question is these effects and interaction
>>> are ready? I dont have to create contrasts manually and which of the
>>> images created I use to the second level analysis?The spmF,spmT or the
>>> con images??
>>> -Having done in the above way the first level analysis which is the
>>> simpliest way to perform second level?Should i  perform an ANOVA within
>>> subjects afterwards or change the contrasts in the first level and
>>> choose another statistical test in the second level?
>>> -I have so many betas because first I chose HRF with derivatives
>>> ,secondly I have 9 conditions plus 6 movement parameters for each
>>> session x 4 sessions ?Could you explain to me what the spmF and spmT
>>> images represent?I imagine the spmF are 4 because threre are one average
>>> effect of condition,two main effects and one interaction effect.Coul i
>>> use then in second level analysis instead of con images ?
>>> 
>>> Thank you in advance.
>> 
>> -- 
>> Guillaume Flandin, PhD
>> Wellcome Centre for Human Neuroimaging
>> UCL Queen Square Institute of Neurology
>> London WC1N 3BG
> 
> -- 
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG

-- 
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG

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