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 >> >> 在 2012-11-22 04:22:06，"Douglas N Greve" greve@nmr.mgh.harvard.edu >> 写道： >>>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 >>>> >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>>> mailto: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. >>>> >>>> >>>> >>> >>>> >> >>>> >> -- >>>> >> 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
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 >>> >>> 在 2012-11-22 04:22:06，"Douglas N Greve" greve@nmr.mgh.harvard.edu >>> 写道： >>>>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 >>>>> >>>> Freesurfer@nmr.mgh.harvard.edu >>>>> >>>> mailto: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. >>>>> >>>> >>>>> >>> >>>>> >> >>>>> >> -- >>>>> >> 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 > > >
Dear experts
there is another question: there are factor 1(A,B), factor 2(C,D,E), one continuous variable (age) and gender (M,F). I want to detect the difference among C、D、E. The factor 1(A,B),age and gender (M,F) as covariates. the following is the contrast matrix: ACM, ADM, AEM, BCM, BDM, BEM, ACF, ADF, AEF, BCF, BDF, BEF 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 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 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 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 is correct? 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 >>> >>> 在 2012-11-22 04:22:06，"Douglas N Greve" greve@nmr.mgh.harvard.edu >>> 写道： >>>>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 >>>>> >>>> Freesurfer@nmr.mgh.harvard.edu >>>>> >>>> mailto: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. >>>>> >>>> >>>>> >>> >>>>> >> >>>>> >> -- >>>>> >> 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 > > >
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xiangbo_2010