There are two options:
(1) Use the tmap to compute the r-values and report the peak r-value:
fslmaths tmap -sqr tmap_sqr
fslmaths tmap_sqr -add N tmap_sqr_df
fslmaths tmap_sqr -div tmap_sqr_df -sqrt rvalue
*N should be replaced by the df.
(2) Use SPSS to determine the r-value of the cluster. The caveat is
that you shouldn't base your inferences on the r-value here because
you've used the data to select the region. However, it is useful for
people who require an r or r-squared value on a plot. The concern is
that if your cluster is not significant after correcting for multiple
comparisons AND you use SPSS to find the r-value and determine its
significant, then you would have a biased result. The important thing
to understand is that your inferences about correlation of a cluster
should be based on the maps and the thresholded map, while the r-value
can be reported via SPSS. Because you are not making inferences on the
SPSS results, you will not be at risk for double dipping.
Hope this clarifies the concern
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
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On Fri, Aug 10, 2012 at 11:40 AM, Rosalia Dacosta <[log in to unmask]> wrote:
> Dear Donald,
>
> Because I need the correlation value (r). With cluster I only get the size
> of the cluster, the significance 1-P and the MNI coordinates (anatomical
> region)...but what about r value?
>
> Warm regards,
>
> Rosalia.
> 2012/8/10 MCLAREN, Donald <[log in to unmask]>
>
>> I'm not quite sure why you'd need SPSS, unless your trying to get the
>> cluster average. Once you have the T-map, you can get the r-value for
>> every voxel. The cluster correlations should not be used to make the
>> conclusions as you have basically thresholded the data, so it would be
>> considered double-dipping.
>>
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>> and
>> Harvard Medical School
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Website: http://www.martinos.org/~mclaren
>> Office: (773) 406-2464
>> =====================
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or
>> agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of
>> any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at
>> (773)
>> 406-2464 or email.
>>
>>
>> On Fri, Aug 10, 2012 at 11:32 AM, Rosalia Dacosta <[log in to unmask]>
>> wrote:
>> > Dear Tibor,
>> >
>> > Thank you very much :)
>> >
>> > Rosalia.
>> >
>> > 2012/8/10 Auer, Tibor <[log in to unmask]>
>> >
>> >> Dear Rosalia,
>> >>
>> >>
>> >>
>> >> Yes.
>> >>
>> >>
>> >>
>> >> Cheers,
>> >>
>> >>
>> >>
>> >> Auer, Tibor M.D. Ph.D.
>> >>
>> >> Biomedizinische NMR Forschungs GmbH
>> >>
>> >> am Max-Planck Institut für Biophysikalische Chemie
>> >>
>> >> Am Fassberg 11
>> >>
>> >> 37077 Göttingen
>> >>
>> >> Germany
>> >>
>> >> Phone/Work: +49-(0)551-201-1725
>> >>
>> >> Phone/Home: +49-(0)551-387-0076
>> >>
>> >> Mobile: +49-(0)176-8012-7921
>> >>
>> >> Mail: [log in to unmask]
>> >>
>> >>
>> >>
>> >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> >> Behalf
>> >> Of Rosalia Dacosta
>> >> Sent: Friday, August 10, 2012 5:14 PM
>> >> To: [log in to unmask]
>> >> Subject: Re: [FSL] A little problem with correlations with Melodic
>> >>
>> >>
>> >>
>> >> Dear Tibor,
>> >>
>> >>
>> >>
>> >> Many thanks for your reply. I am going to try now.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Once I have done this, is it right to do cluster, flsmaths and
>> >> fslmeants
>> >> to get the values for every subject and then introduce them to SPSS in
>> >> order
>> >> to get the r value?
>> >>
>> >>
>> >>
>> >> Warm regards,
>> >>
>> >>
>> >>
>> >> Rosalia.
>> >>
>> >>
>> >
>> >
>> >
>
>
>
>
>
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