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Dear Venkat

The contrasts you have mentioned are t contrasts.
You have mentioned 10 separate t contrasts.
Each contrast will have a separate name.

It is perhaps more correct to first investigate if there are any difference within groups using F contrast and then perform only those t tests which are relevant to your hypothesis. In a full factorial design, the t tests are essentially post hoc analyses.
Both the SPM and VBM manuals will help you develop a better understanding of the statistics.

I am afraid I could not check your design matrix as your earlier mail did not have any attached design matrix picture/figure.

Best wishes
Raka



From: "Rajagopalan, Venkateswaran" <[log in to unmask]>
To: raka maitra <[log in to unmask]>
Sent: Fri, December 17, 2010 5:17:41 PM
Subject: RE: [SPM] VBM stats - question

VBM stats - question
Thanks Raka,
 
There is one question I would like to clarify Now the contrast manager window pops up after run estimate after how would I enter the contrast it is not accepting the numbers if I enter them as per the guidelines given in VBM8 manual
 
I would like test the following contrasts my groups are N (control), C, B,D and E
 
N C B D E
 
1 -1 0 0 0
1 0 -1 0 0
1 0 0 -1 0
1 0 0 0 -1
0 1 -1 0 0
0 1 0 -1 0
0 1 0 0 -1
0 0 1 -1 0
0 0 1 0 -1
0 0 0 1 -1
 
When I enter the above it after choosing F or t-contrast (I tried both) it says too long not a valid number.
 
Thanks
 
Venkat


From: raka maitra [mailto:[log in to unmask]]
Sent: Thu 12/16/2010 7:51 PM
To: Rajagopalan, Venkateswaran; [log in to unmask]
Subject: Re: [SPM] VBM stats - question

Hi

If you have 5 independent groups, then in the 'full factorial' model, you're attempting 1 X 5 one way Anova.
In that case you'll specify the following:
factor 1
levels 5
cell 1 1
      1 2
      1 3
      1 4
      1 5

Within each 'cell' specify smoothed images that belong to the relevant group. e.g for cell 1 1 specify smoothed images of group1, cell 1 2 specify smoothed images of group2, etc

Once you have specified all files, click 'run'
When SPM has processed and given you the design matirx as output, click 'estimate'. This will generate the relevant SPM.mat that you can use for 'results'
(Please note that you will have to specify 'contrasts' once you click 'resulIts')

It would help if you provided more details on what your groups are and what are you trying to investigate.


Hope this helps
Best wishes
Raka





From: "Rajagopalan, Venkateswaran" <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, December 16, 2010 9:29:29 PM
Subject: [SPM] VBM stats - question

Hi All,

I am trying to run stats on my smoothed images after VBM procedure. I am encountering following difficulties

1) I am following steps described in VBM8 manual, I have 5 groups and I want to run one way ANOVA (simple ANOVA no covariates or anything) on it. As recommended in VBM8 manual I am unable to run "full factorial model" I think because I haven't specified any factors in it so it is not running so I choose One way ANOVA from the menu and could get SPM.mat file after this I am unable to define contrast matrix I don't know why?. I followed the steps in VBM8 manual go to SPM menu then Results choose SPM.mat file created from above step after this contrast manager is not opening instead of this a small window pops up asking the following question " This model has not been estimated would you like to estimate it now?. Kindly help me here.

2) I assume that the above one way ANOVA and full factorial model is based on GRF so If I want to run nonparametric stats on my smoothed images I should use SnPM am I right?

Thanks

Venkat

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Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2009).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law. If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited. If
you have received this communication in error, please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy. Thank you.