Re: [Freesurfer] Contrast matrix for PVR

On 08/31/2017 02:30 PM, Martin Juneja wrote: > Hi experts, > > I have a follow up question: > In case I wanted to add another covariate in contrast matrix e.g. in > addition to age and gender if I want to add BMI as another covariate > in calculating correlation between volume and LGI (as menti

Re: [Freesurfer] Contrast matrix for PVR

Hi experts, I have a follow up question: In case I wanted to add another covariate in contrast matrix e.g. in addition to age and gender if I want to add BMI as another covariate in calculating correlation between volume and LGI (as mentioned in previous email), could you please confirm if followi

Re: [Freesurfer] Contrast matrix format {Disarmed}

the two groups. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Wednesday, May 31, 2017 3:12:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format {Disarmed} What p-values are you comparing to? You should run the analysis wi

Re: [Freesurfer] Contrast matrix format {Disarmed}

> of the cortical thickness for each individual subject in a > specific cluster. > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > *Sent:* Friday, May 26, 2017 5:38:35 PM > *To:* freesurfer@n

Re: [Freesurfer] Contrast matrix format {Disarmed}

ect in a specific cluster. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Friday, May 26, 2017 5:38:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format {Disarmed} Aren't your p-values sig?

Re: [Freesurfer] Contrast matrix format {Disarmed}

7 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Contrast matrix format {Disarmed} > It does not matter whether you used the maxvox or the mean of the > cluster. The two p-values are measuring fundamentally different > phenomena. The cluster pvalue is measuring t

Re: [Freesurfer] Contrast matrix format {Disarmed}

d.edu on behalf of Douglas N Greve Sent: Friday, May 26, 2017 12:50:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format {Disarmed} It does not matter whether you used the maxvox or the mean of the cluster. The two p-values are measuring fundamentally diff

Re: [Freesurfer] Contrast matrix format {Disarmed}

aring the > p-values to the cluster wise p-values. > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > *Sent:* Thursday, May 25, 2017 6:06:30 PM > *To:* freesurfer@nmr.mgh.

Re: [Freesurfer] Contrast matrix format {Disarmed}

uglas N Greve Sent: Thursday, May 25, 2017 6:06:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format {Disarmed} Not sure what you did. Sound like you found the max vox from the cluster, then extracted the values from each subject and ran those values through the glm

Re: [Freesurfer] Contrast matrix format {Disarmed}

y, May 25, 2017 2:43:35 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Contrast matrix format > > After some digging I found this thread where someone was having a > similar issue, so I can give this matlab code you posted a try. > > > htt

Re: [Freesurfer] Contrast matrix format {Disarmed}

: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format After some digging I found this thread where someone was having a similar issue, so I can give this matlab code you posted a try. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32951.html

Re: [Freesurfer] Contrast matrix format {Disarmed}

of Douglas Greve Sent: Wednesday, May 24, 2017 10:47:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format yes, that is correct On 5/24/17 10:38 AM, Taylor Hilton wrote: Hi all, I’m trying to perform a group analysis according to the tutorial on this page

Re: [Freesurfer] Contrast matrix format {Disarmed}

10:47:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format yes, that is correct On 5/24/17 10:38 AM, Taylor Hilton wrote: Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki

Re: [Freesurfer] Contrast matrix format

yes, that is correct On 5/24/17 10:38 AM, Taylor Hilton wrote: Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis For my own analysis, I have 4 total groups, and I’m trying to do a contr

[Freesurfer] Contrast matrix format

Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis For my own analysis, I have 4 total groups, and I’m trying to do a contr

Re: [Freesurfer] Contrast matrix regressing out effect of diagnosis and age

yes On 05/19/2017 03:02 AM, Erik Lindberg wrote: > Dear Freesurfer experts, > > I am running a GLM-model in which I have 6 classes (diagnosis) and two > covariates age and variable X). > > I want to look at mean correlation of variable X. > > My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0

[Freesurfer] Contrast matrix regressing out effect of diagnosis and age

Dear Freesurfer experts, I am running a GLM-model in which I have 6 classes (diagnosis) and two covariates age and variable X). I want to look at mean correlation of variable X. My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0 0 0 0.17 0.17 0.17 0.17 0.17 0.17 0.17 (approx. 1/6) Did I get

Re: [Freesurfer] Contrast matrix for PVR

The 2nd is the correct matrix On 5/15/17 12:36 PM, Sahil Bajaj wrote: Hi everyone, From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as fo

[Freesurfer] Contrast matrix for PVR

Hi everyone, >From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as following: GroupDescriptorFile 1 Class Male Class Female Variables Age Inp

Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

-thickness_Fmatrix.glmdir 3. mri_glmfit-sim mri_glmfit-sim --glmdir dx4subgroups_n146-lh-thickness_Fmatrix.glmdir --cache 1.3 abs --cwp 0.05 --2spaces Do you see any issues? Thank you so much for your help! Best, Andrea Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4

Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

That four group test will yield the same exact result as 1 -1 0 0 1 0 -1 0 1 0 0 -1 so I think you are ok On 02/21/2017 03:09 PM, Gold, Andrea (NIH/NIMH) [F] wrote: > > Hi, > > I am trying to run a cortical thickness analysis comparing four groups > – my goal is to conduct an omnibus F-test

[Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

Hi, I am trying to run a cortical thickness analysis comparing four groups – my goal is to conduct an omnibus F-test testing for any group differences. I have 0 covariates/nuisance regressors. This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for 3 groups: https://sur

Re: [Freesurfer] Contrast matrix for per-vertex regressor

Hi Elisa, can you send the command line and full terminal output? doug On 7/4/13 11:50 AM, Elisa Scariati wrote: Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting fo

[Freesurfer] Contrast matrix for per-vertex regressor

Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting for age and gender that worked perfectly. However, when I tried to make a between groups comparison, I ran into an error

Re: [Freesurfer] contrast matrix

On Wed, Mar 27, 2013 at 2:53 AM, xiangbo_2010 wrote: > Dear Prof Donald McLaren > > I am sorry to disturb you! I have four discrete variables {factor 1(A,B), > factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable > (age), I want to use the GLM to analysis the result of the int

[Freesurfer] contrast matrix

Dear Prof Donald McLaren I am sorry to disturb you! I have four discrete variables {factor 1(A,B), factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable (age), I want to use the GLM to analysis the result of the interaction among factor 1(A,B), factor 2(C,D) and factor 3(E,

[Freesurfer] contrast matrix

Dear Prof Donald McLaren I am sorry to disturb you! I have four discrete variables {factor 1(A,B), factor 2(C,D), factor 3(E,F), and gender(M,F)} and a continuous variable (age), I want to use the GLM to analysis the result of the interaction among factor 1(A,B), factor 2(C,D) and factor 3(E,

Re: [Freesurfer] contrast matrix

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 wrote: >> Dear Donald McLaren >> >>I used the contrast to run, but the error is appear: >> >> mri_glmfit --y lh.gender_age.thic

Re: [Freesurfer] contrast matrix

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/~mc

Re: [Freesurfer] contrast matrix

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" 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 variable

Re: [Freesurfer] contrast matrix

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 acc

Re: [Freesurfer] contrast matrix

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

Re: [Freesurfer] contrast matrix

On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve 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

Re: [Freesurfer] contrast matrix

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. If there is an effect in both males and females but the effects go in opposite directions, then the 4 row

Re: [Freesurfer] contrast matrix

Yes, that -BPM should be +BPM, sorry about that. It will not change the p-values if you multiply by 0.5 or not. It will change the size of the contrast. Most people don't report this number, especially for an F-test, so I would not worry about it. doug On 11/20/2012 09:17 AM, xiangbo_2010 wrote

Re: [Freesurfer] contrast matrix

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. S

Re: [Freesurfer] contrast matrix

Dear doug Thank you for your reply! +AOM -BOM -APM -BPM00000 +AOM -BOM00 -AQM +BQM000 +AOM0 -APM000 -COM +CPM0 +AOM000 -AQ

Re: [Freesurfer] contrast matrix

Hi Doug, Thanks for replying. Yet I have a question on this matrix. From what I see, each row corresponds to one contrast, which has one df. Thus why are we having 8 rows while the interaction has a df of 4? Thanks, Cherry On Sun, Nov 18, 2012 at 6:23 PM, Douglas Greve wrote: > > Hi Bo, you can

Re: [Freesurfer] contrast matrix

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

Re: [Freesurfer] contrast matrix

Dear Cherry I our analysis, the gender as a Covariate, so all female groups assigned 0 in the matrix, following is new matrix: 1 -1 -1 -1 -1 -1 0 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 1-1 -1 0 -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 0 0 0

Re: [Freesurfer] contrast matrix

Hi Bo, I'm definitely not an expert of this, but I see that you really nead some help, so I tried to look at your matrix. From my humble opinion it doesn't look correct. Firstly, the first 9 groups are male groups and the last 9 are female groups. Then why are all female groups assigned 0 in the m

[Freesurfer] contrast matrix

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:

[Freesurfer] contrast matrix

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:

Re: [Freesurfer] contrast matrix

That contrast will do what you want but a more general one would be [1 -1 0 0 0 0 0 0 0 0 0 0] [0 0 0 1 -1 0 0 0 0 0 0 0] [1 0 -1 0 0 0 0 0 0 0 0 0] [0 0 0 1 0 -1 0 0 0 0 0 0] This will return positive if there is any difference between the genotypes regardless of gender. In your contrast, you c

[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I wa

[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1)

[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I wa

Re: [Freesurfer] Contrast matrix

Use the significant clusters as ROIs doug On 09/07/2012 10:43 AM, Meng Li wrote: > Hi professor, > Thanks for your letter. > When I perform the analysis of interaction by using the matrix： > 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 0 0 > I get the significant clus

Re: [Freesurfer] Contrast matrix

That is the correct matrix to use. You can create a new FSGD file (and the second matrix would be correct for it), but you do not have to. It will save you a few degrees of freedom. doug On 09/07/2012 05:49 AM, Meng Li wrote: > Hi professor, > Thanks for your reply. > When I perform the main

Re: [Freesurfer] Contrast matrix

Hi professor, Thanks for your reply. When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a

Re: [Freesurfer] contrast matrix

On 09/06/2012 04:42 AM, Meng Li wrote: > Hi Freesurfer experts, > When I perform the statistical analysis, I am very confused with the > following questions: > > My experimental design includes 3 discrete factors: diagnosis with two > levels (A, B); genotype with two levels (G, T); gender (F, M

[Freesurfer] contrast matrix

Hi Freesurfer experts, When I perform the statistical analysis, I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF,

[Freesurfer] contrast matrix

Hi Freesurfers, My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regress

Re: [Freesurfer] contrast matrix

:22 -0400 > From: Douglas N Greve > Subject: Re: [Freesurfer] contrast matrix > To: freesurfer@nmr.mgh.harvard.edu > Hi Meng, the first row is what you want. The second row tests for an > interaction between diagnosis, genotype, and age. > doug > On 08/04/2012 10:23 PM, Meng Li

Re: [Freesurfer] contrast matrix

Hi Meng, the first row is what you want. The second row tests for an interaction between diagnosis, genotype, and age. doug On 08/04/2012 10:23 PM, Meng Li wrote: > Hi Freesurfers, > > My experimental design includes 3 discrete factors and 1 continuous > variables: > > Discrete factors: diagnosi

[Freesurfer] contrast matrix

Hi Freesurfers, My experimental design includes 3 discrete factors and 1 continuous variables: Discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) Continuous variable: age So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want

[Freesurfer] contrast matrix

Hi Freesurfers, My experimental design includes 3 discrete factors and 1 continuous variables: Discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) Continuous variable: age So I can get 8 classes. Then I want to perform 2 (diagnosis)* 2(genotype)

Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

raction > effect. > > Many thanks again. > Jose > > - Mensaje original - > De: Douglas N Greve > Fecha: Martes, 18 de Enero de 2011, 16:53 > Asunto: Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 > continuous variables > A: Jose Luis Ca

Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

, One Covariate. DODS only. QDEC-able) and that I don't have to add any extra zero per covariate when testing the interaction effect. Many thanks again. Jose - Mensaje original - De: Douglas N Greve Fecha: Martes, 18 de Enero de 2011, 16:53 Asunto: Re: [Freesurfer] contrast matrix for

Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

Hi Jose, with 6 classes and 3 continuous variables, I think you should have 24 regressors, which means 24 columns in the contrast matrix. Yours only has 18. Otherwise the contrast to test between B and C is correct (just need to add 6 zeros). For the interaction, you would need 0 0 0.5 -0.5 -0.

[Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

- Dear Freesurfers,   My experimental design includes 2 discrete factors and 3 continuous variables:   Discrete factors: -   Diagnosis with three levels (A, B, C) -   Gender with two levels (Males, Females)   Continuous variables: -   Mean cortical

Re: [Freesurfer] contrast matrix of 2 factors (2x4 groups)

It would be the same as your 2nd matrix with the right four columns negated. doug Stefan Brauns wrote: > Hi all, > > I am trying to examine the interaction of 2 factors (2 x 4 groups) > and have difficulties to find the right contrast matrix for mri_glmfit. > > We have patients and controls at f

[Freesurfer] contrast matrix of 2 factors (2x4 groups)

Hi all, I am trying to examine the interaction of 2 factors (2 x 4 groups) and have difficulties to find the right contrast matrix for mri_glmfit. We have patients and controls at four different aquisition sites and want to know if the changes (i.e. thickness) between patients and controls are equ

Re: [Freesurfer] contrast matrix question

Just to clarify what exactly do you mean by "interaction"? ("interaction" is a somewhat nebulous term, as indicated by Doug's and mine differing responses). If you want to look for a difference in slopes of two main continuous effects, then a contrast vector can indeed be set up to handle that (a

Re: [Freesurfer] contrast matrix question

Oops, Mike is right, disregard my previous email. doug Michael Harms wrote: > Hi Tori, > There is no way to investigate the interaction of two continuous effects > with the contrast vector alone, if the design matrix itself only > involves main effect terms. The interaction itself needs to be co

Re: [Freesurfer] contrast matrix question

Hi Tori, There is no way to investigate the interaction of two continuous effects with the contrast vector alone, if the design matrix itself only involves main effect terms. The interaction itself needs to be coded into the design matrix. Note that it can become tricky as to the proper coeffici

Re: [Freesurfer] contrast matrix question

0 1 1 will just be the mean of the slopes of var1 and var2. Looks like you want 0 1 -1 to look for the interaction. doug Victoria Williams wrote: > Hello, > > I apologize if this is a very simple question, but how would you set up a > contrast matrix to look at the interaction of 2 variables on

[Freesurfer] contrast matrix question

Hello, I apologize if this is a very simple question, but how would you set up a contrast matrix to look at the interaction of 2 variables on a measure? For example, my fsgd file contains: class=1 variables=2 Input Subjid class var1 var2 When I tried using a contrast of 0_1_1 the significance

Re: [Freesurfer] contrast matrix

Hi, I think that I know what you mean. So, if I want to get the result with A > B > C, I should get A > B and B > C, respectively. And then, to combine these two results. Would you tell me detail with step by step and what command I should type and how to type ? Or, have some reference to fol

Re: [Freesurfer] contrast matrix

You can't do that with a contrast matrix. In general, you can't test "ANDs" with a contrast, you have to test "ORs". For AND, you have to use a conjunction in which you make two contrasts A > B and B > C, threshold both (mri_binarize), then do a logical AND. doug Feng-Xian wrote: Hi, I wan

[Freesurfer] contrast matrix

Hi, I want to analysis three independence groups. And, I want to display a result of A group > B group > C group with positive(red) and A group < B group < C group with negative(blue). To show that, how do I write the number of columns in the contrast matrix? Thank you in advance! Feng-X