You can use a fixed effects analysis to combine them. All you need to do is
create a contrast that spans all 5 sessions/runs.
1/5 0 1/5 0 1/5 0 1/5 0 1/5 0 0 0 0 0 0 for 5 sessions with 2 conditions.
Just make sure the contrast weights sun to 1 for the positive coefficients
and -1 for the negative coefficients.
Concatenate is potentially bad if you don't account for the fact that you
have multiple runs. If you properly account for the runs, then its okay;
however, its not worth scripting the analysis to get the proper run effects
in the HP filter, AR(1) estimation, or HRF.
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 Thu, Oct 31, 2013 at 1:36 PM, YAN Chao-Gan <[log in to unmask]> wrote:
> By the way, how to perform 1st level analysis across sessions?
> I.e., I have one subject performed the same task for 5 sessions (or some
> may call them runs). How can I combine them to have one single t map? Use
> some fix effect analysis?
>
> I think it's not a good idea to simply concatenate all the 5 sessions,
> right?
>
> Thanks in advance!
>
> Best,
>
> Chao-Gan
>
>
> On Thu, Oct 31, 2013 at 1:32 PM, YAN Chao-Gan <[log in to unmask]> wrote:
>
>> Thanks Don!
>>
>> It's a two sample t test, the variance is default to be unequal. Then
>> there should be some special process on SPM.xX.Bcov, right?
>>
>> Best,
>>
>> Chao-Gan
>>
>>
>> On Thu, Oct 31, 2013 at 12:22 PM, MCLAREN, Donald <
>> [log in to unmask]> wrote:
>>
>>> Did you set the variance to be equal?
>>>
>>> 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 Thu, Oct 31, 2013 at 11:45 AM, YAN Chao-Gan <[log in to unmask]>wrote:
>>>
>>>> Thanks!
>>>>
>>>> Now I am using SPM.xX.Bcov directly, thus got the same results as
>>>> spm_results_ui.
>>>>
>>>> TData =
>>>> (beta_0001*Contrast(1)+beta_0002*Contrast(2))./(sqrt(ResMS*(Contrast*SPM.xX.Bcov*Contrast')));
>>>>
>>>> In the case of 2nd level statistical analysis, there should be no
>>>> filtering issue, right? Why SPM.xX.Bcov is slightly different
>>>> from (X'*X)^(-1)?
>>>>
>>>> >>SPM.xX.Bcov
>>>> 0.0656 0
>>>> 0 0.0438
>>>> >>(X'*X)^(-1)
>>>> 0.0625 0
>>>> 0 0.0455
>>>>
>>>> Is this caused by an whitening issue?
>>>>
>>>> Thanks,
>>>>
>>>> Chao-Gan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Oct 31, 2013 at 10:44 AM, MCLAREN, Donald <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> xX.xKXs = spm_sp('Set',spm_filter(xX.K,W*xX.X)); % K*W*X
>>>>>
>>>>> Also,
>>>>> xX.xKXs.X = full(xX.xKXs.X);
>>>>> xX.pKX = spm_sp('x-',xX.xKXs); %
>>>>> projector/pseudo-inverse
>>>>> xX.Bcov = xX.pKX*xX.V*xX.pKX';
>>>>>
>>>>> 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 Thu, Oct 31, 2013 at 10:41 AM, YAN Chao-Gan <[log in to unmask]>wrote:
>>>>>
>>>>>> Thanks, Guillaume and Donald! I will read that.
>>>>>>
>>>>>> Hi Donald, what's K in your expression? Seems SPM.xX.K is a struct
>>>>>> which cannot be multiplied:
>>>>>>
>>>>>> >> SPM.xX.K
>>>>>>
>>>>>> ans =
>>>>>>
>>>>>> HParam: 128
>>>>>> row: [1x215 double]
>>>>>> RT: 1.4000
>>>>>> X0: [215x4 double]
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Chao-Gan
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Oct 31, 2013 at 10:31 AM, MCLAREN, Donald <
>>>>>> [log in to unmask]> wrote:
>>>>>>
>>>>>>> Try using:
>>>>>>> pinv(K*W*X)*xX.V*pinv(K*W*X)' instead of (X'*X^(-1))
>>>>>>>
>>>>>>> Then you should get the correct solution.
>>>>>>>
>>>>>>> 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 Wed, Oct 30, 2013 at 11:03 PM, YAN Chao-Gan <[log in to unmask]>wrote:
>>>>>>>
>>>>>>>> And here is an example based on 1st level results. The differences
>>>>>>>> in T values are pretty big, although the pattern is similar.
>>>>>>>>
>>>>>>>> I think I missed something in the code?
>>>>>>>> *TData = (beta_0001*Contrast(1)+beta_0002*Contrast(2))./(sqrt(
>>>>>>>> ResMS*(Contrast*(X'*X)^(-1)*Contrast')));*
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Chao-Gan
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Oct 30, 2013 at 10:50 PM, YAN Chao-Gan <[log in to unmask]>wrote:
>>>>>>>>
>>>>>>>>> Dear SPM experts,
>>>>>>>>>
>>>>>>>>> Recently I would like to calculate the values based on the
>>>>>>>>> estimated files (skip spm_results_ui), I followed the formulas in Page 20
>>>>>>>>> of www.fil.ion.ucl.ac.uk/~mgray/Presentations/2nd level analysis-
>>>>>>>>> Design contrast & inference.ppt<http://www.fil.ion.ucl.ac.uk/~mgray/Presentations/2nd%20level%20analysis-%20Design%20contrast%20&%20inference.ppt>
>>>>>>>>>
>>>>>>>>> X=SPM.xX.X;
>>>>>>>>> Contrast=[1 -1];
>>>>>>>>> TData =
>>>>>>>>> (beta_0001*Contrast(1)+beta_0002*Contrast(2))./(sqrt(ResMS*(Contrast*(X'*X)^(-1)*Contrast')));
>>>>>>>>>
>>>>>>>>> However, the results (Left in the attached figure) is slightly
>>>>>>>>> different from the results generated by spm_results_ui (Right in the
>>>>>>>>> attached figure). Furthermore, seems this difference is even bigger when
>>>>>>>>> applied to 1st level results (maybe due to the hidden high-pass filtering
>>>>>>>>> regressors?)
>>>>>>>>>
>>>>>>>>> I am wondering if the differences are caused simply by data
>>>>>>>>> precision, or I made something wrong in the above code?
>>>>>>>>>
>>>>>>>>> Thanks a lot for your time and help in advance!
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Chao-Gan
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Chao-Gan YAN, Ph.D.
>>>>>>>>> Research Scientist
>>>>>>>>> The Nathan Kline Institute for Psychiatric Research, 140 Old
>>>>>>>>> Orangeburg Road, Orangeburg, NY 10962
>>>>>>>>> Center for the Developing Brain, Child Mind Institute, 445 Park
>>>>>>>>> Avenue, New York, NY 10022
>>>>>>>>> The Phyllis Green and Randolph Cowen Institute for Pediatric
>>>>>>>>> Neuroscience, New York University Child Study Center, New York, NY 10016
>>>>>>>>> -
>>>>>>>>> Initiating + Service Node
>>>>>>>>> The R-fMRI Network (RFMRI.ORG)
>>>>>>>>> *http://rfmri.org/yan*
>>>>>>>>> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Chao-Gan YAN, Ph.D.
>>>>>>>> Research Scientist
>>>>>>>> The Nathan Kline Institute for Psychiatric Research, 140 Old
>>>>>>>> Orangeburg Road, Orangeburg, NY 10962
>>>>>>>> Center for the Developing Brain, Child Mind Institute, 445 Park
>>>>>>>> Avenue, New York, NY 10022
>>>>>>>> The Phyllis Green and Randolph Cowen Institute for Pediatric
>>>>>>>> Neuroscience, New York University Child Study Center, New York, NY 10016
>>>>>>>> -
>>>>>>>> Initiating + Service Node
>>>>>>>> The R-fMRI Network (RFMRI.ORG)
>>>>>>>> *http://rfmri.org/yan*
>>>>>>>> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Chao-Gan YAN, Ph.D.
>>>>>> Research Scientist
>>>>>> The Nathan Kline Institute for Psychiatric Research, 140 Old
>>>>>> Orangeburg Road, Orangeburg, NY 10962
>>>>>> Center for the Developing Brain, Child Mind Institute, 445 Park
>>>>>> Avenue, New York, NY 10022
>>>>>> The Phyllis Green and Randolph Cowen Institute for Pediatric
>>>>>> Neuroscience, New York University Child Study Center, New York, NY 10016
>>>>>> -
>>>>>> Initiating + Service Node
>>>>>> The R-fMRI Network (RFMRI.ORG)
>>>>>> *http://rfmri.org/yan*
>>>>>> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Chao-Gan YAN, Ph.D.
>>>> Research Scientist
>>>> The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg
>>>> Road, Orangeburg, NY 10962
>>>> Center for the Developing Brain, Child Mind Institute, 445 Park Avenue,
>>>> New York, NY 10022
>>>> The Phyllis Green and Randolph Cowen Institute for Pediatric
>>>> Neuroscience, New York University Child Study Center, New York, NY 10016
>>>> -
>>>> Initiating + Service Node
>>>> The R-fMRI Network (RFMRI.ORG)
>>>> *http://rfmri.org/yan*
>>>> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>>>>
>>>
>>>
>>
>>
>> --
>> Chao-Gan YAN, Ph.D.
>> Research Scientist
>> The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg
>> Road, Orangeburg, NY 10962
>> Center for the Developing Brain, Child Mind Institute, 445 Park Avenue,
>> New York, NY 10022
>> The Phyllis Green and Randolph Cowen Institute for Pediatric
>> Neuroscience, New York University Child Study Center, New York, NY 10016
>> -
>> Initiating + Service Node
>> The R-fMRI Network (RFMRI.ORG)
>> *http://rfmri.org/yan*
>> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>>
>
>
>
> --
> Chao-Gan YAN, Ph.D.
> Research Scientist
> The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg
> Road, Orangeburg, NY 10962
> Center for the Developing Brain, Child Mind Institute, 445 Park Avenue,
> New York, NY 10022
> The Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience,
> New York University Child Study Center, New York, NY 10016
> -
> Initiating + Service Node
> The R-fMRI Network (RFMRI.ORG)
> *http://rfmri.org/yan*
> http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
>
