Dear Stefano,
OK, I see. Thanks for your help.
All the best.
2013-12-06
Rujing Zha
发件人：<std...@virgilio.it>
发送时间：2013-12-05 22:34
主题：R: Re: [Freesurfer] R: Re: R: Re: Linear regression
收件人："charujing123"<charujing...@163.com>,"freesurfer"<freesurfer@nmr.mgh.harvard.edu>
抄送：
Dear Rujing,
After recon-all and qcache, for correlation analysis, I have performed qdec by
using a matrix that contains NPS test, 3 nuisance factors and one groups.
For groups analysis I have applied mri_glmfit as described in the guide.
Nothing in particular.
Stefano
----Messaggio originale----
Da: charujing...@163.com
Data: 5-dic-2013 2.15
A: "stdp82"<std...@virgilio.it>, "freesurfer"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: Linear regression
Dear Stefano,
I also want to make a correlation analysis between thickness and behavior data.
Would you please send me your precious scripts for group analysis( unpaired
t-test and correlation analysis) after recon-all? I want to study it if I get
your permission.
Thanks.
All the best.
2013-12-05
Rujing Zha
发件人：<std...@virgilio.it>
发送时间：2013-12-05 02:06
主题：[Freesurfer] R: Re: R: Re: Linear regression
收件人："greve"<gr...@nmr.mgh.harvard.edu>,"freesurfer"<freesurfer@nmr.mgh.harvard.edu>
抄送：
Dear Douglas, thank you very much for you kind reply.
In the paper I have 3 groups (2 diseases and 1 controls).
I have performed cortical thickness analysis among groups, individuating
relevant difference in the posterior regions.
Next, for one group, I have used qdec to individuate statistically significant
regions where NPS test scores and thickness were correlated. 3 nuisance factors
was also added to regressor. All results were corrected for multiple
comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation.
qdec analysis results have individuated a "composite region" (superior parietal
cortex and precuneus) where NPS correlated with thinning.
Now, if I understand, I should extract the mean thickness from superior
parietal cortex and precuneus and I should perform a linear regression (and
partial correlation) with an other statistical program (SPSS for example).
Is there a better way to perform a regression the most possible similar to qdec
computation?
Stefano
----Messaggio originale----
Da: gr...@nmr.mgh.harvard.edu
Data: 4-dic-2013 17.35
A: <std...@virgilio.it>, <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: R: Re: [Freesurfer] Linear regression
On 12/02/2013 03:14 PM, std...@virgilio.it wrote:
> Tank you very much.
>
> A-Do you mean the partial correlation coeff (PCC) at each voxel
> averaged over region?
> Finally a linear regression is done between cortical thickness of a
> composite region and NPS. However the authors discuss every individual
> region as related to disease. So a table with partials correlations of
> individuals ROIs with NPS seems useful to support the discussion.
What did you do in the paper? The reviewer mentions a "composite
region". Did you average the thickness over that region and then do the
regression with NPS?
>
> B- I'd like to obtain the covariance matrix of the regression made
> between cortical thickness, group and covariates. How can I do it?
> I'm not sure what you mean. Would this be a different matrix for each
> vertex?
> I cite the referee: "The authors must provide the covariance matrix of
> the regression made between cortical thickness, group and covariates
> as supplementary information in order to increase the value of the
> results."
Sorry, I don't understand what the reviewer is asking for.
doug
>
> I don't have Matlab for mri_glmfit_pcc matlab.
>
> Stefano
>
>
>
>
> ----Messaggio originale----
> Da: gr...@nmr.mgh.harvard.edu
> Data: 2-dic-2013 20.47
> A: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] Linear regression
>
>
> On 12/02/2013 02:22 PM, std...@virgilio.it wrote:
> > Hi list,
> >
> > I have some questions, please.
> >
> > I performed linear regression by qdec to find the regions where the
> > cortical thinning correlates with neuropsychological test (NPS),
> > taking in account 3 nuisance factors.
> >
> > A- I individuated some posterior regions and now I'd like to build a
> > table with partials correlations of individuals ROIs with NPS. How can
> > I obtain the values for each region?
> Do you mean the partial correlation coeff (PCC) at each voxel averaged
> over region? You can get PCC maps using the mri_glmfit_pcc matlab
> command. You can then do the averaging over region using mri_segstats.
> >
> > B- I'd like to obtain the covariance matrix of the regression made
> > between cortical thickness,group and covariates. How can I do it?
> I'm not sure what you mean. Would this be a different matrix for each
> vertex?
> >
> > C- Is there a specific reference for qdec?
> No, it is just a GLM so any GLM reference will do.
> >
> > Thank you very much,
> >
> >
> > Stefano
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 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
>
>
> 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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
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.
