Dear experts
I want to make interaction among factor 1(A,B), factor 2(C,D,E) and one continuous variable (age), gender (M,F) as covariate, how to design the contrast? thanks!
Bo Xiang
At 2012-12-02 05:24:18,"MCLAREN, Donald" <mclaren.donald@gmail.com> wrote:
>Bo Xiang got the following Error Message. Attached are the mtx and
>fsgd file. Does anyone what caused the error?
>
>>
>>On Fri, Nov 30, 2012 at 8:28 AM, xiangbo_2010 <xiangbo_2010@126.com> wrote:
>>> Dear Donald McLaren
>>>
>>> I used the contrast to run, but the error is appear:
>>>
>>> mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd COMTthreeinteryes.fsgd
>>> dods --C COMTthreeinteryes.mtx --surf fsaverage rh --cortex --glmdir
>>> lh.COMTthree.glmdir
>>>
>>> gdfReadHeader: reading COMTthreeinteryes.fsgd
>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>> Continuous Variable Means (all subjects)
>>> 0 age 26.2227 11.3891
>>> Class Means of each Continuous Variable
>>> 1 MAC 23.9333
>>> 2 MAD 23.5455
>>> 3 MAE 24.5000
>>> 4 MBC 28.6923
>>> 5 MBD 26.3158
>>> 6 MBE 30.3750
>>> 7 FAC 24.1707
>>> 8 FAD 26.4643
>>> 9 FAE 25.0909
>>> 10 FBC 25.9130
>>> 11 FBD 31.5217
>>> 12 FBE 34.0000
>>> INFO: gd2mtx_method is dods
>>> Reading source surface /media/freesurfer1/CT/fsaverage/surf/rh.white
>>> Number of vertices 163842
>>> Number of faces 327680
>>> Total area 65020.765625
>>> AvgVtxArea 0.396850
>>> AvgVtxDist 0.717994
>>> StdVtxDist 0.193566
>>>
>>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
>>> cwd /media/freesurfer1/CT
>>> cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd
>>> COMTthreeinteryes.fsgd dods --C COMTthreeinteryes.mtx --surf fsaverage rh
>>> --cortex --glmdir lh.COMTthree.glmdir
>>> sysname Linux
>>> hostname psylab-desktop
>>> machine x86_64
>>> user psylab
>>> FixVertexAreaFlag = 1
>>> UseMaskWithSmoothing 1
>>> OneSampleGroupMean 0
>>> y /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh
>>> logyflag 0
>>> usedti 0
>>> FSGD COMTthreeinteryes.fsgd
>>> labelmask /media/freesurfer1/CT/fsaverage/label/rh.cortex.label
>>> maskinv 0
>>> glmdir lh.COMTthree.glmdir
>>> IllCondOK 0
>>> ReScaleX 1
>>> DoFFx 0
>>> Creating output directory lh.COMTthree.glmdir
>>> Loading y from /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh
>>> INFO: gd2mtx_method is dods
>>> Saving design matrix to lh.COMTthree.glmdir/Xg.dat
>>> Normalized matrix condition is 82.694
>>> Matrix condition is 73313.7
>>> Found 149926 points in label.
>>> Pruning voxels by thr: 0.000000
>>> Found 149926 voxels in mask
>>> Saving mask to lh.COMTthree.glmdir/mask.mgh
>>> Reshaping mriglm->mask...
>>> search space = 74490.928733
>>> MatrixReadTxT: could not scan value [3][1]
>>>
>>> ERROR: loading C COMTthreeinteryes.mtx
>>>
>>> thanks!
>>>
>>> Bo Xiang
>>>
>>>
>>>
>>>
>>>
>>> At 2012-11-30 06:25:12,"MCLAREN, Donald" <mclaren.donald@gmail.com> wrote:
>>>>Yes.
>>>>
>>>>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, Nov 28, 2012 at 3:27 AM, xiangbo_2010 <xiangbo_2010@126.com> wrote:
>>>>> Dear Donald McLaren
>>>>>
>>>>>>> I want to make interaction between factor 1 (A,B) and factor 2
>>>>>>> (C,D,E).
>>>>>>> age
>>>>>
>>>>>>> and gender (M,F)
>>>>>>> as covariates, I can get 12 classes: ACM ADM AEM BCM BDM BEM ACF ADF
>>>>>>> AEF
>>>>>>> BCF BDF BEF and make the contrast:
>>>>>>>
>>>>>>> +ACM -ADM 0 -BCM +BDM 0 +ACF -ADF 0 -BCF +BDF 0 age age age age age age
>>>>>>> age age age age age age
>>>>>>> 0 +ADM -AEM 0 -BDM +BEM 0 +ADF -AEF 0 -BDF +BEF age age age age age age
>>>>>>> age age age age age age
>>>>> because the age and gender as covariates, the column of age should be
>>>>> instead of 0. the constrast is following:
>>>>>
>>>>> 1 -1 0 -1 1 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>> 0 1 -1 0 -1 1 0 1 -1 0 -1 1 0 0 0 0 0 0 0 0 0 0 0 0
>>>>> is correct? thanks!
>>>>>
>>>>> Bo Xiang
>>>>>
>>>>>
>>>>> At 2012-11-22 11:15:08,"MCLAREN, Donald" <mclaren.donald@gmail.com>
>>>>> wrote:
>>>>>>Please provide us with what each column represents. There seems to be
>>>>>>too many zeros.
>>>>>>
>>>>>>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, Nov 21, 2012 at 7:26 PM, xiangbo_2010 <xiangbo_2010@126.com>
>>>>>> wrote:
>>>>>>> Dear Donald McLaren
>>>>>>>
>>>>>>> I want to make interaction between factor 1 (A,B)and factor 2(C,D,E).
>>>>>>> age
>>>>>>> and gender (M,F)
>>>>>>> as covariates, I can get 12 classes: ACM ADM AEM BCM BDM BEM ACF ADF
>>>>>>> AEF
>>>>>>> BCF BDF BEF and make the contrast:
>>>>>>>
>>>>>>> +ACM -ADM 0 -BCM +BDM 0 +ACF -ADF 0 -BCF +BDF 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>> 0 +ADM -AEM 0 -BDM +BEM 0 +ADF -AEF 0 -BDF +BEF 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>> 0
>>>>>>>
>>>>>>> is correct? thanks!
>>>>>>>
>>>>>>> Bo Xiang
>>>>>>>
>>>>>>>
>>>>>>> At 2012-11-22 08:55:29,"MCLAREN, Donald" <mclaren.donald@gmail.com>
>>>>>>> wrote:
>>>>>>>>Please explain what are the columns represent.
>>>>>>>>
>>>>>>>>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, Nov 21, 2012 at 2:50 PM, <xiangbo_2010@126.com> wrote:
>>>>>>>>> No, I want to compute the interaction between factor 1 and factor 2 ,
>>>>>>>>> gender and age as covariates. thanks
>>>>>>>>>
>>>>>>>>> Bo Xiang
>>>>>>>>>
>>>>>>>>> ÔÚ 2012-11-22 04:22:06£¬"Douglas N Greve" <greve@nmr.mgh.harvard.edu>
>>>>>>>>> дµÀ£º
>>>>>>>>>>Hi Bo, I don't understand the contrast you are trying to make. Are
>>>>>>>>>> you
>>>>>>>>>>really trying to compute the interaction between four variables
>>>>>>>>>> (factor
>>>>>>>>>>1, factor 2, gender, and age)?
>>>>>>>>>>doug
>>>>>>>>>>
>>>>>>>>>>On 11/21/2012 10:49 AM, xiangbo_2010 wrote:
>>>>>>>>>>> Dear Donald McLaren
>>>>>>>>>>> Thank you for your reply! I make the contrast according to your
>>>>>>>>>>> method
>>>>>>>>>>> is following£¬but I want to make interaction between factor 1
>>>>>>>>>>> (A,B)and
>>>>>>>>>>> factor 2(C,D,E), gender (M,F) and one continuous variable (age) as
>>>>>>>>>>> covariates, the following contrast:
>>>>>>>>>>> 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> 0 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>>
>>>>>>>>>>> is correct? Thanks!
>>>>>>>>>>> Bo Xiang
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> At 2012-11-21 04:07:37,"MCLAREN, Donald"<mclaren.donald@gmail.com
>>>>>>>>>>> <mailto:mclaren.donald@gmail.com>> wrote:
>>>>>>>>>>> >On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
>>>>>>>>>>> ><greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>>>>>>>>>>> > wrote:
>>>>>>>>>>> >> Thanks Donald. Is this the standard way to do this? I had used
>>>>>>>>>>> >> 8
>>>>>>>>>>> >> rows
>>>>>>>>>>> >> instead of 4 with the difference being that 8 rows gives you an
>>>>>>>>>>> >> opportunity
>>>>>>>>>>> >> to look for an effect in males OR females.
>>>>>>>>>>> >
>>>>>>>>>>> >Yes. Having 8 rows would tell you if you have an interaction
>>>>>>>>>>> > between
>>>>>>>>>>> >factor 1 and 2 in either males or females. My 4 rows only tell you
>>>>>>>>>>> > if
>>>>>>>>>>> >the interaction exists. Technically speaking, one would run the
>>>>>>>>>>> >three-way interaction first. If nothing existed then you do the
>>>>>>>>>>> >two-way interaction as I suggested. If there is a three-way
>>>>>>>>>>> >interaction, then you would use Doug's approach of the interaction
>>>>>>>>>>> > in
>>>>>>>>>>> >either males or females.
>>>>>>>>>>> >
>>>>>>>>>>> >If there is an effect in both
>>>>>>>>>>> >> males and females but the effects go in opposite directions,
>>>>>>>>>>> >> then
>>>>>>>>>>> >> the 4 row
>>>>>>>>>>> >> implementation will resolve to 0 (no effect). Or am I
>>>>>>>>>>> >> misunderstanding
>>>>>>>>>>> >> something (again:)?
>>>>>>>>>>> >
>>>>>>>>>>> >Nope. You are right. If the male and female effects are different,
>>>>>>>>>>> >then they could cancel each other out. If you suspect this to be
>>>>>>>>>>> > the
>>>>>>>>>>> >case, then you should be able to demonstrate a three-way
>>>>>>>>>>> > interaction.
>>>>>>>>>>> >
>>>>>>>>>>> >> thanks!
>>>>>>>>>>> >> doug
>>>>>>>>>>> >>
>>>>>>>>>>> >>
>>>>>>>>>>> >> On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> Bo,
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> Doug asked me to chime in on your issue. Here are some points
>>>>>>>>>>> >>> that
>>>>>>>>>>> >>> you
>>>>>>>>>>> >>> (and others) will hopefully find useful.
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (1) Inferences are two-step process. First, you create and
>>>>>>>>>>> >>> estimate
>>>>>>>>>>> >>> the design matrix. Every column in the design matrix accounts
>>>>>>>>>>> >>> can
>>>>>>>>>>> >>> account for some of the variance in the data. Second, you have
>>>>>>>>>>> >>> contrasts that allow you to infer specific effects. Because
>>>>>>>>>>> >>> the
>>>>>>>>>>> >>> model
>>>>>>>>>>> >>> contains your covariates, you are always controlling for the
>>>>>>>>>>> >>> covariates and by extension any factor/covariate not in the
>>>>>>>>>>> >>> contrast.
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (2) Forming contrasts is often the most difficult thing to do.
>>>>>>>>>>> >>> I
>>>>>>>>>>> >>> assume that your three factors (1, 2, and gender) are all
>>>>>>>>>>> >>> between-subject factors. If one of them is a within-subject
>>>>>>>>>>> >>> factor
>>>>>>>>>>> >>> please let me know and disregard the rest of the email. The
>>>>>>>>>>> >>> final
>>>>>>>>>>> >>> F-contrast will have 4 rows (factor 1 levels-1)*(factor 2
>>>>>>>>>>> >>> levels
>>>>>>>>>>> >>> -1)=(3-1)*(3-1)=2*2=4
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> The following is an outline for creating contrasts:
>>>>>>>>>>> >>> (a) Start simple - difference between levels of 1 factor
>>>>>>>>>>> >>> (b) Define your null hypothesis: AO=AP=AQ
>>>>>>>>>>> >>> (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
>>>>>>>>>>> >>> (d) Repeat for the other levels of the factor...
>>>>>>>>>>> >>> BO-BP=0 AND BP-BQ=0
>>>>>>>>>>> >>> CO-CP=0 AND CP-CQ=0
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (f) Make them equal to 0:
>>>>>>>>>>> >>> AO-AP-BO+BP=0
>>>>>>>>>>> >>> BO-BP-CO+CP=0
>>>>>>>>>>> >>> AP-AQ-BP+BQ=0
>>>>>>>>>>> >>> BP-BQ-CP+CQ=0
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (g) Expand them to include gender, for example:
>>>>>>>>>>> >>> AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> Since the contrast now has 2 columns per level, you should
>>>>>>>>>>> >>> divide
>>>>>>>>>>> >>> all
>>>>>>>>>>> >>> values by 2. This will produce the correct amplitude and
>>>>>>>>>>> >>> statistics.
>>>>>>>>>>> >>> If you leave the values as 1 and -1, then you will have an
>>>>>>>>>>> >>> incorrect
>>>>>>>>>>> >>> amplitude, but the statistics will still be correct.
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (h) Fill in the respective columns of your design matrix.
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> (3) The degrees of freedom are defined based on the rows of
>>>>>>>>>>> >>> the
>>>>>>>>>>> >>> F-matrix and the number of rows in the design matrix. The
>>>>>>>>>>> >>> F-test
>>>>>>>>>>> >>> has a
>>>>>>>>>>> >>> numerator and denominator degrees of freedom. F(n,d).
>>>>>>>>>>> >>>
>>>>>>>>>>> >>> 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 Tue, Nov 20, 2012 at 8:17 AM,
>>>>>>>>>>> >>> xiangbo_2010<xiangbo_2010@126.com
>>>>>>>>>>> >>> <mailto:xiangbo_2010@126.com>>
>>>>>>>>>>> >>> wrote:
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Dear doug
>>>>>>>>>>> >>>> Thank you for your reply!
>>>>>>>>>>> >>>> +AOM -BOM -APM -BPM 0 0 0 0 0
>>>>>>>>>>> >>>> +AOM -BOM 0 0 -AQM +BQM 0 0 0
>>>>>>>>>>> >>>> +AOM 0 -APM 0 0 0 -COM +CPM 0
>>>>>>>>>>> >>>> +AOM 0 0 0 -AQM -COM 0 +CQM
>>>>>>>>>>> >>>> there should be use 1 -1 or 0.5 -0.5? whether the -BPM should
>>>>>>>>>>> >>>> be
>>>>>>>>>>> >>>> change
>>>>>>>>>>> >>>> BPM?
>>>>>>>>>>> >>>> Thanks
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Bo Xiang
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> At 2012-11-19 07:23:31,"Douglas
>>>>>>>>>>> >>>> Greve"<greve@nmr.mgh.harvard.edu
>>>>>>>>>>> >>>> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Hi Bo, you can think of the Ftest as a logical 'OR' between
>>>>>>>>>>> >>>> the
>>>>>>>>>>> >>>> t-test
>>>>>>>>>>> >>>> contrasts indicated in each row. Each row is a difference of
>>>>>>>>>>> >>>> differences,
>>>>>>>>>>> >>>> so
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 1. (A-B)om - (A-B)pm --> Does the difference between A and
>>>>>>>>>>> >>>> B
>>>>>>>>>>> >>>> differ
>>>>>>>>>>> >>>> between
>>>>>>>>>>> >>>> groups O and P for Males?
>>>>>>>>>>> >>>> 2. (A-B)om - (A-B)qm
>>>>>>>>>>> >>>> 3. (A-C)om - (A-C)pm
>>>>>>>>>>> >>>> 4. (A-C)om - (A-C)qm
>>>>>>>>>>> >>>> 5. (A-B)of - (A-B)pf --> Does the difference between A and
>>>>>>>>>>> >>>> B
>>>>>>>>>>> >>>> differ
>>>>>>>>>>> >>>> between
>>>>>>>>>>> >>>> groups O and P for Females?
>>>>>>>>>>> >>>> 6. (A-B)of - (A-B)qf
>>>>>>>>>>> >>>> 7. (A-C)of - (A-C)pf
>>>>>>>>>>> >>>> 8. (A-C)of - (A-C)pf
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> I've put together the first 9 columns of the first 4 rows.
>>>>>>>>>>> >>>> The
>>>>>>>>>>> >>>> last 9
>>>>>>>>>>> >>>> columns are all 0s. For the last for rows, the 0s and below
>>>>>>>>>>> >>>> matrix are
>>>>>>>>>>> >>>> swapped to give you the same for the females
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> doug
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> AOM BOM APM BPM AQM BQM COM CPM CQM
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> --------------------------------------------------------------------------
>>>>>>>>>>> >>>> +AOM -BOM -APM -BPM 0 0 0 0 0
>>>>>>>>>>> >>>> +AOM -BOM 0 0 -AQM +BQM 0 0 0
>>>>>>>>>>> >>>> +AOM 0 -APM 0 0 0 -COM +CPM 0&! nbsp;&nb sp;
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> +AOM 0 0 0 -AQM -COM 0 +CQM
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> On 11/17/12 9:21 PM, xiangbo_2010 wrote:
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Hi Freesurfer experts,
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> I'm very sorry to bother you, but I am very confused with the
>>>>>>>>>>> >>>> following
>>>>>>>>>>> >>>> questions:
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> My experimental design includes three discrete factors:
>>>>>>>>>>> >>>> factor
>>>>>>>>>>> >>>> 1
>>>>>>>>>>> >>>> with
>>>>>>>>>>> >>>> three
>>>>>>>>>>> >>>> levels (A,B,C ); factor 2 with three levels (O,P,Q); gender
>>>>>>>>>>> >>>> (F,
>>>>>>>>>>> >>>> M), and
>>>>>>>>>>> >>>> one
>>>>>>>>>>> >>>> covariate.
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> So I can get 18 classes: FAO,
>>>>>>>>>>> >>>> FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO,
>>>>>>>>>>> >>>> MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the
>>>>>>>>>>> >>>> interaction
>>>>>>>>>>> >>>> between
>>>>>>>>>>> >>>> factor 1 and factor 2 regressing out the effect of gender and
>>>>>>>>>>> >>>> one
>>>>>>>>>>> >>>> covariate,
>>>>>>>>>>> >>>> but I don't know the rules for setting the contrasts for the
>>>>>>>>>>> >>>> F-test. The
>>>>>>>>>>> >>>> contrast matrix I used is:
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>> 0 0 0 0
>>>>>>>>>>> >>>> 0
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> is it correct?
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Any help will be very appreciated.
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Best wishes,
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> Bo Xiang
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> _______________________________________________
>>>>>>>>>>> >>>> Freesurfer mailing list
>>>>>>>>>>> >>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>>> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>> _______________________________________________
>>>>>>>>>>> >>>> Freesurfer mailing list
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>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>>
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>>>>>>>>>>> >>>> properly
>>>>>>>>>>> >>>> dispose of the e-mail.
>>>>>>>>>>> >>>>
>>>>>>>>>>> >>>
>>>>>>>>>>> >>
>>>>>>>>>>> >> --
>>>>>>>>>>> >> Douglas N. Greve, Ph.D.
>>>>>>>>>>> >> MGH-NMR Center
>>>>>>>>>>> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>>>>>>>>> >> Phone Number: 617-724-2358
>>>>>>>>>>> >> Fax: 617-726-7422
>>>>>>>>>>> >>
>>>>>>>>>>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>>>>>>>> >> FileDrop: 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
>>>>>>>>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>>greve@nmr.mgh.harvard.edu
>>>>>>>>>>Phone Number: 617-724-2358
>>>>>>>>>>Fax: 617-726-7422
>>>>>>>>>>
>>>>>>>>>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>>>>>>>FileDrop: 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>_______________________________________________
>>>>>>>>Freesurfer mailing list
>>>>>>>>Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>