Subject: | | Re: job description (structure) under spm 8 |
From: | | Corinna Vehlow <[log in to unmask]> |
Reply-To: | | [log in to unmask][log in to unmask]> wrote:
Jonathan,
Maybe I'm interpreting Marta's design matrix schematic incorrectly, but doesn't it look like there's an implicit baseline in each of the sessions? (The dark bands in the regressors for the conditions.) If so, that would serve as your "C" below.
Of course, everything you wrote stands on its own.
>Hi Marta > >The problem is that the effect in which you are interested (right vs. >left ankle dorsiflexion) is also a difference between sessions. By >modeling session effects (which is the right thing to do) (columns 3 >and 4 of your design matrix), you essentially remove any overall >difference between sessions, making it difficult or impossible to pull >out differences in your conditions. Put another way, your effects of >interest are confounded with session effects. > >If you have a chance to change the design, you could consider one of >the following alternatives: > >1) Have both conditions of interest in both sessions (i.e. alternate >left and right ankle movements within both sessions). This way you >have the same number of events of each type but they are not related >to session effects. > >2) Have some baseline condition you can compare the ankle dorsiflexion >to. This is no doubt explained in more detail somewhere previously on >the list, but the idea is that it's possible to look at an interaction >across sessions, but not really main effects. I.e. > >Session 1: condition A and condition C >Session 2: condition B and condition C > >contrast A > B is problematic because of session effects; >contrast: (A > C) > (B > C) would be fine. > >If you are stuck with the data as it stands (and no possibility of >finding a baseline condition to add to the model), I don't know if >there is a particularly good solution. You can choose not to model >session effects, but this will add noise, and I think be a bit harder >to interpret (e.g., is higher signal in a region actually due to your >task, or could it just be a byproduct of one session by chance having >a different level of activity than another?). > >Hope this helps, >Jonathan > > >On Tue, Nov 3, 2009 at 11:46 AM, Gandolla Marta ><[log in to unmask]> wrote: >> Hi everyone, >> >> I have some problems in two sessions analysis. I want to compare two >> activation maps from the same subject in two different conditions. I built >> the design matrix with two sessions (using first level analysis) so I ended >> up with four columns as you can see from the first figure of the attached >> file. I then did inference analysis with contrast vector of [1 -1 0 0] and I >> suppose I shoud get a map with the significative differences between the two >> conditions. >> my problem is that if I implement this same approach with maps that are >> significantly different for sure (right ankle dorsiflexion and left ankle >> dorsiflexion) I get a "difference map" that is not at all as expected. so as >> you can see what I'm talking about, the second figure of the attached file >> is the result I got.40_3Nov200922:30:[log in to unmask] |
Date: | | Mon, 2 Nov 2009 08:22:27 +0100 |
Content-Type: | | text/plain |
Parts/Attachments: |
|
|
|
|
Hi Brahim,
thanks for your answer. That sounds first of all good, but how can I
do the first step and create it manually?
Thanks for your help
Best wishes
Corinna
Zitat von Brahim HAMADICHAREF <[log in to unmask]>:
>
> Hi Corinna
>
>
>
> I would
>
>
>
> 1 - Create one example manually and then save it as MyJob.mat
>
> 2 - Load the MyJob.mat into MATLAB and expand all the fields of
>
> the structure to see the default values and specific ones of
>
> your example.
>
> 3 - Modify the job (in MATLAB script format) to your needs, for
>
> e.g. path and values can be given as parameters ...
>
> 4 - Run it as batch
>
>
> Regards
>
>
> Brahim
>
>> Date: Sun, 1 Nov 2009 22:00:58 +0100
>> From: [log in to unmask]
>> Subject: [SPM] job description (structure) under spm 8
>> To: [log in to unmask]
>>
>> Hi,
>>
>> for those who already read the mail with the subject: matlab (batch)
>> scripts with spm8, can stop here. I send the mail twice (with
>> different subjects) as I was not sure, which one fits better and will
>> bring results/answers. Sorry for that!
>>
>> I'd like to write a Matlab script that performs all the spatial
>> processing steps after each other, starting with conversion of Dicom
>> files, realignment, over coregistration, estimation of the
>> transformation warp and finally normalisation. We want to use it, to
>> transform anatomical and functional brain data into MNI space. I have
>> a script, which was written to work with spm5, but it doesn't work
>> with spm8.
>> Does anybody know how the job-descriptions (variable) has to look like
>> under spm8? So what structure should it have for the different tasks
>> (conversion from dicom to analyze, realigment, coregistration etc.)? I
>> couldn't find a documentation or anything about thsi on the spm webside.
>>
>> Hope someone can help.
>> Thanks a lot in advance.
>>
>> Best wishes
>> Corinna
>
>
> _________________________________________________________________
> Windows 7: Find the right PC for you. Learn more.
> http://windows.microsoft.com/shop
|
|
|
|