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Subject:

Re: model & contrast

From:

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Reply-To:

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Date:

Fri, 1 Dec 2000 12:54:40 GMT

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text/plain (118 lines)

Dear Gregory,

As I understand it, in your experimental design you have two groups (Normal Controls and Patients).
You want construct a design matrix in which your stimulus is represented as ON for 4 blocks (40 scans duration), and the first block starts at scan 14. All the others scans occur during the OFF condition.

I assume that you are primarily interested in localising areas in which there is an interaction between Stimulus state (ON vs. OFF) and Group (Normal vs. Patient).

You should therefore construct a design matrix that includes all your subjects from both groups (e.g. subjects 1-10, nomal; subjects 11-20, patient).

For a given subject, the simplest way of analysing this data would be to represent ON and OFF in the same column.

To acheive this, you should specify the number of trial types as 1 (instead of 2). Then,

Stochastic Design, NO.
SOA, variable.
vector of onsets, [enter onset times of ON blocks] In your case, this is 14 94 174 254
variable durations, NO.
parametric modulation, NONE.
Are these trials: EPOCHS.
Select type of response: e.g. Box-car.
Convolve with hrf: e.g. YES....
Epoch length, 40
Interactions among trials, NO

User specified regressors [1]...
Enter user speficied regressor [if you have any]...

The second part of your enquiry relates to contrasts.

On vs. OFF for single subject (first level analysis):
For a given subject, if you wanted to find areas in which activity related to ON was greater than activity related to OFF, you would use a t-contrast of +1. To find areas where the inverse was true, you would simply use the contrast -1.

Group x Condition Interaction (second level analysis):
In order ro arrive at a meaningful interaction result, you would really need to perform a random effects analysis on the Con images derived from the first level analyses of each subject. to derive a meaningful result for the interaction. There are several previous emails in the archives relating to how this is done practically.

I hope this is helpful. If you wish, I could send you an email of the SPM_fMRIDexMtx.mat file for a single subject.

Best wishes,

Narender Ramnani

___________________________________
Narender Ramnani, PhD.

University Laboratory of Physiology,
University of Oxford.

FMRIB Centre
John Radcliffe Hospital
Oxford.
___________________________________



In message  <[log in to unmask]> Gregory Krolczyk <[log in to unmask]> writes:
> SPMers help!
>
> I am a new spm user, and I trying to come up with a fMri experimental model
> and contrast. Please see if my logic is at fault/imcomplete. I have tried
> your on line tutorials and mailing list archives.
>
> My experiment consists of on (stimulus) and off times. In terms of frames,
> the breakdown is
>
> Condition       Frames  length
> OFF             1-13    13
> ON              14-53   40
> OFF             54-93   40
> ON              94-133  40
> OFF             134-173 40
> ON              174-213 40
> OFF             214-253 40
> ON              254-293 40
> OFF             294-319 25
>
> My first problem is with the experimental model. I'm looking for a checkered
> pattern ie
>
> M
> M
> M
> M
>
> but have not achieved one when I fill SPM in as follows...
>
> Interscan interval 2.24
> scans 319
> trails 2
> SOA variable
> vector on 14 94 174 254
> vector off 1 54 134 214 294
> NO variable durations
> epoch lengths on 40
> epoch lengths off 13 40 40 40 25
> regressors 0
>
> PROBLEM, when I look at the fmri design for off, epoch lenth for off is
> 13... not 13 40 40 40 25... Why is that....?
>
> Remedy... have three variables with the first being just 1-13 (off)
> The second being the on's
> The third being the rest of the off's
>
>
> Problem two (clarification)...
>
> I now want to take my model and form contrasts. I have 10 normals and I
> would like to compare to each and every diseased...
>
> would the contrasts be
>
> -1/10 0 <---nine more of these.... 1 0
>
> note -1/10 represents the on period
>
> _____________________________________________________________________________________
> Get more from the Web.  FREE MSN Explorer download : http://explorer.msn.com

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