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
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.
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
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 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
Hi Antonelle, the way you have have it set up, C = [+1 -1] will be positive (red) for Class1>Class2 and negative (blue) for Class2>Class1. Your fsgd file looks ok.
doug
Antonella Kis wrote:
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
mailto:fischl@nmr.mgh.harvard.edu>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com> *Cc:* "freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Douglas N Greve