Hi Doug and many thanks for your reply and help. If blue means neg, red/yellow is positive does this means that where is blue we have a decrease in FA for while positive means an increase?
How I know if there is a decrease in controls versus patients and not opposite (FA decreases in patients versus controls)?

Is my  C = +1.00000 -1.00000 correct if I am interested only in group differences and I want to eliminate the age.

Also can you please take a look on my y (please see the attached file) to confirm if is correct?


Thank you very much and have a great weekend!
Antonella
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>; freesurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, January 13, 2012 2:13 PM
Subject: Re: Fw: [Freesurfer] FA and non_FA group analysis

Look at the original sig map. This will be signed (blue and red/yellow), with blue being neg, red/yellow being positive.
doug

Antonella Kis wrote:
> Dear Doug,
>
> I am forwarding Bruce answer to my question since he directed me to you.
>
> I need some help regarding my FA and non-FA group analysis study. I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register.  I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmfit-sim with the option grf as you recommended me some time ago:
>
>  mri_glmfit-sim \
>    --glmdir Group_Analysis.glmdir \
>    --grf 2 neg \
>    --cwpvalthresh .025 \
>    --overwrite
>  to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if  my FA is increasing or decreasing in controls
>  group versus patients group.
> 
> I will appreciate any help/suggestion.
>
>  Thank you.
>  Antonella
>
> ----- Forwarded Message -----
> *From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <atorok9@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Thursday, January 12, 2012 11:16 AM
> *Subject:* Re: [Freesurfer] FA and non_FA group analysis
>
> Hi Antonella
>
> I think this is a question for Doug.
>
>
> cheers
> Bruce
> On Thu, 12 Jan 2012, Antonella Kis
> wrote:
>
> >
> >
> > Dear Bruce,
> >
> > Once again many thanks for helping.I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register.  I used the GLM group
> > analysis method after I concatenate FA from individuals into one file and used
> >
> >
> > mri_glmfit-sim \
> >  --glmdir Group_Analysis.glmdir \
> >  --grf 2 neg \
> >  --cwpvalthresh .025 \
> >  --overwrite
> >
> > to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if  my FA is increasing or decreasing in controls
> > group versus patients group.
> >
> >
> > Please advise me.
> >
> > Thank you.
> > Antonella
> >
> >
> >
> >
> >
> >
> >
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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