Dear FreeSurfers,
I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds.
My understanding is that I should perform a surface based group analysis with freesurfer.
I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
Would anyone had some tips to build the Fsgd file and the contrast file ?
Thank you very much in advance.
Best,
Charles
there is a tutorial with similar variables available here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Oct 5, 2016 at 9:22 AM, charles laidi medcharleslaidi@gmail.com wrote:
Dear FreeSurfers,
I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds.
My understanding is that I should perform a surface based group analysis with freesurfer.
I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
Would anyone had some tips to build the Fsgd file and the contrast file ?
Thank you very much in advance.
Best,
Charles
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.
This is a straightforward extension to the FSGD examples. You have 3 discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 2*2*6=24 classes. With one covariate, you would have 24 covariate regressors (one for each class) for a total of 48. You would then need to create a contrast matrix that tests for an interaction between diagnosis and age which is also a straight-forward extension to the examples.
Having said that, I think that 48 regressors is a lot unless you have about 500 subjects. It is also possible to have a less agressive model and just have two regressors, one for each diagnosis. But you'd have to create the design matrix yourself as this is outside of the FSGD specification.
On 10/05/2016 09:22 AM, charles laidi wrote:
Dear FreeSurfers,
I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds.
My understanding is that I should perform a surface based group analysis with freesurfer.
I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
Would anyone had some tips to build the Fsgd file and the contrast file ?
Thank you very much in advance.
Best,
Charles
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas and Trisanna,
Thank you very much for your explanations.
I just would like to be sure of what I am doing since there is no example on the wiki as complex as mine.
If I have the following classes :
Diagnosis : Patient or Control Gender : Male or Female Site : Site1 or Site2 or Site3
NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24 Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes intercept for Group 1 Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes intercept for Group 2 Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes intercept for Group 3 .... Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes intercept for Group 12 Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age slope for Group 1 Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age slope for Group 2 ... Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes age slope for Group 12
*I assume my FSGDF file should look like : *
GroupDescriptorFile 1 Title analysis Class PatientMaleSite1 Class PatientMaleSite2 Class PatientMaleSite3 Class PatientFemaleSite1 Class PatientFemaleSite2 Class PatientFemaleSite3 Class ControlMaleSite1 Class ControlMaleSite2 Class ControlMaleSite3 Class ControlFemaleSite1 Class ControlFemaleSite2 Class ControlFemaleSite3 Variables Age Input subject1 PatientMaleSite1 30 Input subject2 PatientFemaleSite2 45 Input subject3 PatientFemaleSite3 85 Input subject4 PatientFemaleSite4 75 ...
As for the contrast analysis :
If my question is : *is there a difference between Patient and Controls age slope regressing out the effects of gender and site? *
*Contrast1 patient-control.slope.mtx*
0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5
with all regressor1 to regressor12 equal to *0* with regressor13 to 18 equal to *0.5 *(regressor with Patient in it) with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)
If my question is :* is there a difference between cortical thickness in patients and controls, regressing out the effects of age, gender and site ? *
*Contrast2 patient-controls.mtx*
0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0
with all regressor1 to regressor6 equal to *0.5*with all regressor7 to regressor12 equal to -*0.5* with all regressor13 to regressor24 equal to *0*
Thank you very much in advance for your help and sorry for taking your time.
Best,
Charles
2016-10-05 17:44 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
This is a straightforward extension to the FSGD examples. You have 3 discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 2*2*6=24 classes. With one covariate, you would have 24 covariate regressors (one for each class) for a total of 48. You would then need to create a contrast matrix that tests for an interaction between diagnosis and age which is also a straight-forward extension to the examples.
Having said that, I think that 48 regressors is a lot unless you have about 500 subjects. It is also possible to have a less agressive model and just have two regressors, one for each diagnosis. But you'd have to create the design matrix yourself as this is outside of the FSGD specification.
On 10/05/2016 09:22 AM, charles laidi wrote:
Dear FreeSurfers,
I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds.
My understanding is that I should perform a surface based group analysis with freesurfer.
I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
Would anyone had some tips to build the Fsgd file and the contrast file ?
Thank you very much in advance.
Best,
Charles
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 greve@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.
Both contrasts are right. You might want to change the value from 0.5 to 1/6, but that won't affect the actual p-values (only the gamma values). The 2nd contrast is correct, but it maybe difficult to interpret if the first contrast has an effect. Technically, you should verify that there is no interaction between group and continuous covariates. If there is no effect, then re-run with DOSS (the non-interaction model).
On 10/12/16 1:01 PM, charles laidi wrote:
Dear Douglas and Trisanna,
Thank you very much for your explanations.
I just would like to be sure of what I am doing since there is no example on the wiki as complex as mine.
If I have the following classes :
Diagnosis : Patient or Control Gender : Male or Female Site : Site1 or Site2 or Site3
NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24 Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes intercept for Group 1 Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes intercept for Group 2 Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes intercept for Group 3 .... Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes intercept for Group 12 Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age slope for Group 1 Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age slope for Group 2 ... Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes age slope for Group 12
*I assume my FSGDF file should look like : *
GroupDescriptorFile 1 Title analysis Class PatientMaleSite1 Class PatientMaleSite2 Class PatientMaleSite3 Class PatientFemaleSite1 Class PatientFemaleSite2 Class PatientFemaleSite3 Class ControlMaleSite1 Class ControlMaleSite2 Class ControlMaleSite3 Class ControlFemaleSite1 Class ControlFemaleSite2 Class ControlFemaleSite3 Variables Age Input subject1 PatientMaleSite1 30 Input subject2 PatientFemaleSite2 45 Input subject3 PatientFemaleSite3 85 Input subject4 PatientFemaleSite4 75 ...
As for the contrast analysis :
If my question is : *is there a difference between Patient and Controls age slope regressing out the effects of gender and site? *
_Contrast1 patient-control.slope.mtx_
0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5
with all regressor1 to regressor12 equal to *0* with regressor13 to 18 equal to *0.5 *(regressor with Patient in it) with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)
If my question is :*is there a difference between cortical thickness in patients and controls, regressing out the effects of age, gender and site ? *
_Contrast2 patient-controls.mtx_
0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0
with all regressor1 to regressor6 equal to *0.5 *with all regressor7 to regressor12 equal to -*0.5* with all regressor13 to regressor24 equal to *0*
Thank you very much in advance for your help and sorry for taking your time.
Best,
Charles
2016-10-05 17:44 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
This is a straightforward extension to the FSGD examples. You have 3 discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 2*2*6=24 classes. With one covariate, you would have 24 covariate regressors (one for each class) for a total of 48. You would then need to create a contrast matrix that tests for an interaction between diagnosis and age which is also a straight-forward extension to the examples. Having said that, I think that 48 regressors is a lot unless you have about 500 subjects. It is also possible to have a less agressive model and just have two regressors, one for each diagnosis. But you'd have to create the design matrix yourself as this is outside of the FSGD specification. On 10/05/2016 09:22 AM, charles laidi wrote: > Dear FreeSurfers, > > I would like to study the interaction between age and cortical > thickness in patients and controls. > My hypothesis is that there is an interaction and that cortical > thickness is decreasing faster with age in patients than in controls. > I have both Male and Female included in 6 different centers. > I would like to consider also Gender and Site (6 centers) as confounds. > > My understanding is that I should perform a surface based group > analysis with freesurfer. > > I am not able to find an example for my problem in the documentation > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V> > > Would anyone had some tips to build the Fsgd file and the contrast file ? > > Thank you very much in advance. > > Best, > > Charles > > > > _______________________________________________ > 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> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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 <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/ <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 <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
freesurfer@nmr.mgh.harvard.edu
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charles laidi -
Douglas Greve -
Douglas N Greve
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Trisanna Sprung-Much