I tried correlations and the 2nd derivative is definitely not orthogonal.
>> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
ans =
1.0000 -0.0000 -0.5427
-0.0000 1.0000 -0.0298
-0.5427 -0.0298 1.0000
I looked at the regressors that SPM generates for the same data:
ans =
1.0000 0.0436 0.1740
0.0436 1.0000 -0.0226
0.1740 -0.0226 1.0000
The first derivative is not as orthogonal but the second derivative was much
more orthogonal.
Does this have to do with what you noted below about how the second derivative
is being calculated?
So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of
statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdie...@mac.com> wrote:
> Thanks for the quick response! So if I wanted to use the Calhoun 2004
> approach, I should be able to use the Steffener 2010 correction to address
> the violation of the assumption that the regressors were standardized and
> generate a new beta.nii.gz file where the primary beta values have been
> replaced with the Calhoun 2004 measure. Can I assume the three regressors
> are more or less orthogonal? I got non-zero numbers when I tried to test the
> assumption in the Xtmp.X variable
>
> sum(X(1:207,4).*X(1:207,5))
>
> but not hugely non-zero so maybe just rounding errors?
>
>
> On Jul 9, 2013, at 4:16 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> On 07/09/2013 04:11 PM, Joseph Dien wrote:
>>> Hi,
>>> I have a question about how mkcontrast-sess works. I ran an
>>> analysis using the mkanalysis-sess option spmhrf 2 so there are three
>>> regressors for each predictor, the primary, the latency, and the
>>> dispersion. When specifying the contrast weights for mkcontrast-sess,
>>> the documentation indicates that they are specified in terms of the
>>> conditions as numbered in the paradigm file, not the individual
>>> regressors. Furthermore there only appears to be one contrast value
>>> output for each contrast, not three.
>>>
>>> How are the three regressors being handled? I can think of several
>>> scenarios:
>>>
>>> 1) the contrast weights are not actually in terms of conditions (the
>>> documentation is incorrect), they are actually in terms of the
>>> regressors (so contrasting conditions 1 and 2 could be specified as -a
>>> 1 -a 2 -a 3 -c 4 -c 5 -c 6).
>>>
>>> 2) the latency and dispersion regressors are being ignored (a common
>>> practice). The contrast weights should therefore be specified as -a 1
>>> -c 2.
>> This is what happens. If you want to use the derivatives, then you need
>> to spec -setwdelay. When you run the command, it will prompt you for 3
>> values to use. If you spec 1 0 0, then it will be the same as the
>> default. If you want to test only the first derivative, then you would
>> spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time,
>> not the first derivative wrt the dispersion parameter. You cannot get
>> the Calhoun 2004 value using a contrast (it is non-linear).
>> doug
>>>
>>> 3) The Calhoun et al (2004) approach is being used to combine the
>>> three regressors into a "derivative boost" amplitude
>>> measure. The contrast weights should therefore be specified as -a 1 -c 2.
>>>
>>> Thanks for any help you can give me!
>>>
>>> Joe
>>>
>>> --------------------------------------------------------------------------------
>>>
>>> Joseph Dien,
>>> Senior Research Scientist
>>> University of Maryland
>>>
>>> E-mail: jdie...@mac.com <mailto:jdie...@mac.com>
>>> Phone: 202-297-8117
>>> http://joedien.com//
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> University of Maryland
>
> E-mail: jdie...@mac.com
> Phone: 202-297-8117
> http://joedien.com//
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
