Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

2024-05-08 Thread Douglas N. Greve 
They are not identical, for  sure. In general, I discourage people from 
modeling categorical variables (eg, Group1/2 below) as continuous 
variables because you make assumptions that might not be reasonable (eg, 
females will have twice the thickness as males). I would use the first 
method.


On 5/2/2024 8:20 PM, Lydia Chung wrote:


External Email - Use Caution

Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which 
regions show differences in cortical thickness between group 1 and 
group 2) and 2) interaction effects (does the relationship between IV 
and DV depend on moderator). Depending on the model, the IV is 
sometimes a binary categorical variable and sometimes a continuous 
variable. The moderator is always continuous. So, interaction effects 
are either continuous x continuous OR categorical x continuous.


One thing I'm trying to understand is whether the two examples below 
are basically two different approaches that answer the SAME question: 
Do people in Group 1 differ from Group 2 on cortical thickness? 
Version 1 is the one provided by FS and Version 2 is an analog of 
another setup I have been provided by colleagues. Are these models 
answering the same or different questions? The freesurfer link below 
also shows an example of how to do an interaction (Group x Age) using 
Version 1 setup; for Version 2 setup of an interaction, I know I would 
multiply the IV and Moderator before this step so that I would have an 
additional "interaction variable" column to add as one of the 
'Variables' listed in the fsgd code.  So, I'm also curious if the two 
different methods of testing an interaction (in addition to the first 
question about the main effect) will get you the identical answer OR 
if there is something conceptually different? Do the nuances of this 
setup have to do with the difference between using DODS or DOSS?


_
_
_Main effect of Group on cortical thickness Version 1 (copied from FS 
example. link here 
)_

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like 
an anova approach?)


_Main effect of Group on cortical thickness Version 2_
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a 
linear regression approach?)


Thank you in advance for your help!

Lydia
--


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 

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[Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

2024-05-02 Thread Lydia Chung 
External Email - Use Caution

Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which regions
show differences in cortical thickness between group 1 and group 2) and 2)
interaction effects (does the relationship between IV and DV depend on
moderator). Depending on the model, the IV is sometimes a binary
categorical variable and sometimes a continuous variable. The moderator is
always continuous. So, interaction effects are either continuous x
continuous OR categorical x continuous.

One thing I'm trying to understand is whether the two examples below are
basically two different approaches that answer the SAME question: Do people
in Group 1 differ from Group 2 on cortical thickness? Version 1 is the one
provided by FS and Version 2 is an analog of another setup I have been
provided by colleagues. Are these models answering the same or different
questions? The freesurfer link below also shows an example of how to do an
interaction (Group x Age) using Version 1 setup; for Version 2 setup of an
interaction, I know I would multiply the IV and Moderator before this step
so that I would have an additional "interaction variable" column to add as
one of the 'Variables' listed in the fsgd code.  So, I'm also curious if
the two different methods of testing an interaction (in addition to the
first question about the main effect) will get you the identical answer OR
if there is something conceptually different? Do the nuances of this setup
have to do with the difference between using DODS or DOSS?


*Main effect of Group on cortical thickness Version 1 (copied from FS
example. link here 
)*
GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like an
anova approach?)

*Main effect of Group on cortical thickness Version 2*
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a linear
regression approach?)

Thank you in advance for your help!

Lydia
-- 


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 



*Confidentiality Text:*

The information contained in this e-mail message may be privileged,
confidential, and/or protected from disclosure. This e-mail message may
contain protected health information (PHI); dissemination of PHI should
comply with applicable federal and state laws. If you are not the intended
recipient, or an authorized representative of the intended recipient, any
further review, disclosure, use, dissemination, distribution, or copying of
this message or any attachment (or the information contained therein) is
strictly prohibited. If you think that you have received this e-mail
message in error, please notify the sender by return e-mail and delete all
references to it and its contents from your systems.
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.