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
Input zerek1 Male 21
Input zerek2 Male 25
etc.
My concern is:
To run mri_glmfit command, I am not sure how to define my contrast matrix if I am interested in removing the effect of age and sex.
1st option I tried is: 0 0.5 0.5 0 1
Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error.
2nd option I tried is: 0 0 0 0 1
This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix?
Thank you so much !
Best,
Sahil
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 following:
GroupDescriptorFile 1
Class Male
Class Female
Variables Age
Input zerek1 Male 21
Input zerek2 Male 25
etc.
My concern is:
To run mri_glmfit command, I am not sure how to define my contrast matrixif I am interested in removing the effect of age and sex.
1st option I tried is: 0 0.5 0.5 0 1
Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error.
2nd option I tried is: 0 0 0 0 1
This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix?
Thank you so much !
Best,
Sahil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 following contrast matrix is correct:
*0 0 0 0 0 0 1*
for FSGD:
GroupDescriptorFile 1
Class Male
Class Female
Variables Age BMI
Input zerek1 Male 21 17
Input zerek2 Male 25 19
etc. If that's the correct matrix, could you please briefly explain how this matrix explains the effect of age, sex and BMI i.e. how does each zero and 1 explain the correlation between volume and LGI and removes the effect of age, sex and BMI?
Thanks.
On Tue, May 16, 2017 at 8:31 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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 following:
GroupDescriptorFile 1
Class Male
Class Female
Variables Age
Input zerek1 Male 21
Input zerek2 Male 25
etc.
My concern is:
To run mri_glmfit command, I am not sure how to define my contrast matrix if I am interested in removing the effect of age and sex.
1st option I tried is: 0 0.5 0.5 0 1
Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error.
2nd option I tried is: 0 0 0 0 1
This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix?
Thank you so much !
Best,
Sahil
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
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 mentioned in previous email), could you please confirm if following contrast matrix is correct:
*0 0 0 0 0 0 1*
that is correct
for FSGD:
GroupDescriptorFile 1
Class Male
Class Female
Variables Age BMI
Input zerek1 Male 21 17
Input zerek2 Male 25 19
etc.
If that's the correct matrix, could you please briefly explain how this matrix explains the effect of age, sex and BMI i.e. how does each zero and 1 explain the correlation between volume and LGI and removes the effect of age, sex and BMI?
This is a contrast matrix, so it does not explain anything. It is the columns in the design matrix that will explain effects. Each column means something and each column gets a regression coefficient. By setting the corresponding value in the contrast mat to 0 you tell mri_glmfit to to fit/account for that column in the design but do not include it in the contrast
Thanks.
On Tue, May 16, 2017 at 8:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 following: GroupDescriptorFile 1 Class Male Class Female Variables Age Input zerek1 Male 21 Input zerek2 Male 25 etc. My concern is: To run mri_glmfit command, I am not sure how to define my contrast matrixif I am interested in removing the effect of age and sex. 1st option I tried is: 0 0.5 0.5 0 1 Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error. 2nd option I tried is: 0 0 0 0 1 This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix? Thank you so much ! Best, Sahil _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas N Greve
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Sahil Bajaj