Continue with what you have done, do not model it as a continuous variable.
doug

On 06/02/2015 04:03 PM, Matthieu Vanhoutte wrote:
> Dear Experts,
>
> I have run GLM group analyses with Freesurfer tools according DODS 
> model, with six classes ((Male,Female) ; (Control,Left,Right)) and one 
> age variable :
>
> /Class MaleControl
> Class MaleLeft
> Class MaleRight
> Class FemaleControl
> Class FemaleLeft
> Class FemaleRight
> Variables Age
>
> /However, I would like to consider gender as covariable of my GLM 
> design. So, should I as done consider gender as discret factor and 
> part of CLASS/group or should I consider gender as a continuous 
> variable (0 = male, 1 =  female) and add a column on the Variables 
> line of the FSGD file near Age (/Variables Age Gender) ?
>
> /Many thanks in advance for helping !
>
> Best regards,
> Matthieu/
> /
>> On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:
>>> Hello,
>>>
>>> I have run GLM group analyses with Freesurfer tools according DODS 
>>> model, with six classes ((Male,Female) ; (Control,Left,Right)) and 
>>> one age variable :
>>>
>>> /Class MaleControl
>>> Class MaleLeft
>>> Class MaleRight
>>> Class FemaleControl
>>> Class FemaleLeft
>>> Class FemaleRight
>>> Variables Age /
>>>
>>> I wanted to test /Control > Left/ and /Control > Right/ on CBF maps. 
>>> I defined with help of the tutorial contrats for that :
>>>
>>> /control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
>>> control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0
>>> control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0
>>> control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5/
>>>
>>> My problem is that I don't know how to interpret significative 
>>> results in both /Control > Left /contrasts/: 
>>> //control-left.intercept.mtx /and///control-left.slope.mtx. /The 
>>> same for/Control > Right./ One is coding for intercept and the other 
>>> for slope, but concretely what significative results in both 
>>> contrasts mean ?
>>>
>>> Thank you in advance for helping !
>>>
>>> Best regards,
>>>
>>> -------------------------------------
>>> Matthieu Vanhoutte, MSc
>>> Research Engineer - Department of Neuroradiology
>>> Regional University Hospital, Lille, France
>>>
>>> 2015-03-11 16:51 GMT+01:00 Douglas N Greve 
>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>:
>>>
>>>
>>>     the sig value is actually      -log10(p)*sign(gamma) where gamma
>>>     is the
>>>     contrast (gamma.mgh). The p-value is two-tailed, and the color
>>>     indicates
>>>     what tail you are on.
>>>     doug
>>>
>>>     On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
>>>     > Dear FreeSurfer's experts,
>>>     >
>>>     > I have launched a GLM analyses following the tutorial :
>>>     > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>     >
>>>     > Below the command I have used :
>>>     >
>>>     > /mri_glmfit \
>>>     >   --y
>>>     >
>>>     
>>> ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
>>>     > \
>>>     >   --fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
>>>     >   --C
>>>     ${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
>>>     >   --surf fsaverage lh \
>>>     >   --cortex \
>>>     >   --glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
>>>     >
>>>     >
>>>     > In order to see the uncorrected results with p<.0001, I ran :
>>>     >
>>>     > /freeview -f
>>>     > 
>>> ${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
>>>     > -viewport 3d/
>>>     >
>>>     > However, nothing appears with this threshold and when I wanted to
>>>     > configure overlay I saw that most of my values in /sig.mgh /were
>>>     > negatives between -4 and 0...
>>>     >
>>>     > How is possible for /-log10(pvalue)/ values ? Could I obtain
>>>     > significant uncorrected values from this /sig.mgh/ file ?
>>>     >
>>>     > Please find attached my needed files : *y.fsgd, mri_glmfit.log,
>>>     > **/control-left.intercept.mtx/ and sig.mgh *
>>>     >
>>>     > Thank you in advance for helping me !!
>>>     >
>>>     > Best regards,
>>>     >
>>>     > -------------------------------------
>>>     > Matthieu Vanhoutte, MSc
>>>     > Research Engineer - Department of Neuroradiology
>>>     > Regional University Hospital, Lille, France
>>>     >
>>>     >
>>>     > _______________________________________________
>>>     > Freesurfer mailing list
>>>     > Freesurfer@nmr.mgh.harvard.edu
>>>     <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
>>>     Phone Number: 617-724-2358 <tel:617-724-2358>
>>>     Fax: 617-726-7422 <tel:617-726-7422>
>>>
>>>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>     www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>     <http://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
>>>     <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.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://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.
>
>
>
> _______________________________________________
> 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

Reply via email to