Dear Michael,
Thanks so much for clarifying now I understand better. One last question though as you mentioned my "diagnostic criteria" are actually coding a categorical scale (in my case I can say that it is an ordinal variable but not definitely an interval data) so in this case how can I study the relationship between GM volume changes and this diagnostic criteria.
Thanks a lot
Venkat
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Michael Harms
Sent: Thu 5/19/2011 11:13 AM
To: [log in to unmask]
Subject: Re: [FSL] Contrast matrix-FSL VBM
Ok, I guess I read your email incorrectly then.
Each group EV should contains 1's indicating the members of that group,
and 0's otherwise. Your use of "diagnostic criteria" as EV5 is ok
PROVIDED that the values of that EV constitute an interval scale. If
the values of EV5 are actually coding a categorial scale (see
http://en.wikipedia.org/wiki/Level_of_measurement), then the coding of
EV5 isn't meaningful. If EV5 is indeed a meaningful interval scale,
then the contrast
0 0 0 0 1
would tell you whether there is a significant (+ve) relationship across
all subjects between "diagnostic criteria" and your dependent variable
while controlling for group status.
The contrasts
Ev1 Ev2 Ev3 Ev4 Ev5
1 0 0 0 1
0 1 0 0 1
0 0 1 0 1
0 0 0 1 1
are not testing anything meaningful.
cheers,
-MH
On Thu, 2011-05-19 at 10:51 -0400, Rajagopalan, Venkateswaran wrote:
> Dear Michael,
>
> Thanks I am able understand your answer to some extent. Kindly help me with the following
>
> 4 group EVs, and then a 5th EV in which you code an integer "diagnostic criteria" in which each integer corresponds to a different group
>
> Sorry I am not able to understand here "in which each integer corresponds to a different group"
>
> Here is what I have for each subject in each group I have diagnostic criteria score as given below
>
> patient group 1(EV1) patient group 2 (EV2) ..................diagnostic criteria (Ev5)
> subject 1 GM vol 1
> Subject 2 GM vol 2
> subject 3 GM vol 4
> . subject 1 GM vol 3
> subject 2 GM vol 1
> . . .
> . . .
> . . .
> .
> So If I want to correlate GM volume changes with my diagnostic criteria, how can I design my EVs and contrast matrix. I didn't classify my patients groups based on diagnostic criteria but I classified them based on their clinical phenotype evaluated using clinical signs and symptoms but I am interested to see is there is correlation between GM volume changes and their diagnostic criteria.
>
> Also can you kindly tell me whether my design and contrast matrix is correct for my other clinical criteria disease duration
>
> Ev1 Ev2 Ev3 Ev4 Ev5
> > 0 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> >
> > or
> > Ev1 Ev2 Ev3 Ev4 Ev5
> > 1 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> > 0 1 0 0 1
> > 0 0 1 0 1
> > 0 0 0 1 1
>
> Thanks
>
> Venkat
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Michael Harms
> Sent: Thu 5/19/2011 10:22 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Contrast matrix-FSL VBM
>
>
>
> Hi Venkat,
>
> If I'm reading your email correctly, it sounds as if you have a design
> with 4 group EVs, and then a 5th EV in which you code an integer
> "diagnostic criteria" in which each integer corresponds to a different
> group. If so, then that design doesn't make sense since "diagnostic
> criteria" is already being modeled by your 4 group EVs (and you can't
> model a "class" or "categorical" variable involving more than two levels
> with a single EV anyway).
>
> cheers,
> -MH
>
> On Thu, 2011-05-19 at 09:58 -0400, Rajagopalan, Venkateswaran wrote:
> > Dear All,
> >
> > I read FSL archives and Steve also clarified me with some of my
> > questions but I am not sure about the following contrast matrix which
> > I designed to correlate between clinical measures and GM volume
> > changes. My question here is does the GM volume changes correlate with
> > clinical measures
> >
> > I have 4 groups of patient groups (let us say group1, group2, group3
> > and group4) and I have clinical measures disease duration (in number
> > of months), diagnostic criteria which varies from 1-4 and disease
> > progression
> >
> > As per Steve's suggestion I tried to design a model for each clinical
> > measure for instance for diagnostic criteria of 1-4. My question here
> > does the GM volume change correlate diagnostic criteria. I have 5 EVs
> > with Ev1..Ev4 for patient groups (i.e. their GM volume changes) and
> > Ev5 is the dignostic criteria.Now I would like to know which of the
> > below contrast matrix is correct
> >
> > Ev1 Ev2 Ev3 Ev4 Ev5
> > 0 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> >
> > or
> > Ev1 Ev2 Ev3 Ev4 Ev5
> > 1 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> > 0 1 0 0 1
> > 0 0 1 0 1
> > 0 0 0 1 1
> >
> > OR do I need to model by grouping my patients (my current method of
> > grouping patients is based on their different clinical phenotypes)
> > based on diagnostic criteria i.e. group1 (diagnostic criteria =1),
> > group2 (diagnostic criteria =2)...
> >
> >
> > Similarly for my clinical measure of disease duration
> > 5 EVs with Ev1..Ev4 for patient groups (i.e. their GM volume changes)
> > and Ev5 is the disease duration
> >
> > Ev1 Ev2 Ev3 Ev4 Ev5
> > 0 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> >
> > or
> > Ev1 Ev2 Ev3 Ev4 Ev5
> > 1 0 0 0 1 (for +ve correlation and -1 for -ve correlation)
> > 0 1 0 0 1
> > 0 0 1 0 1
> > 0 0 0 1 1
> >
> > Sorry designs similar to these are discussed in FSL archives
> > unfortunately I am not sure about my contrast matrix.
> >
> > Thanks
> >
> > Venkat
> >
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2010).
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
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