Re: [Freesurfer] Vertex-wise analysis using ComBat

[Douglas N. Greve]

I don't think you can. I have not looked at combat in a long time, but I 
thought they did their own GLM. combat might take a design matrix, in 
which case you could use mri_glmfit and your FSGD to create the design 
matrix.


On 8/30/2022 9:37 AM, Rene Seiger wrote:


External Email - Use Caution

Dear FreeSurfer community!

We collected structural data from different scanners and we want to 
conduct a surface-based (vertex-wise) analysis in FreeSurfer using 
predefined regions of interest. The model is quite simple, as we just 
want to correlate a specific (e.g. behavioral) measurement from all 
subjects (one group) with the thickness on the surface in specific 
ROIs. To account for the different scanner types, we are planning to 
use ComBat to account for this effect. However, we are not quite sure 
how and at which stage we could implement ComBat using the standard 
FreeSurfer FSGD file approach. Any help would be highly appreciated, 
Thanks!



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[Freesurfer] Vertex-wise analysis using ComBat

[Rene Seiger]

   External Email - Use Caution


Dear FreeSurfer community!

We collected structural data from different scanners and we want to 
conduct a surface-based (vertex-wise) analysis in FreeSurfer using 
predefined regions of interest. The model is quite simple, as we just 
want to correlate a specific (e.g. behavioral) measurement from all 
subjects (one group) with the thickness on the surface in specific ROIs. 
To account for the different scanner types, we are planning to use 
ComBat to account for this effect. However, we are not quite sure how 
and at which stage we could implement ComBat using the standard 
FreeSurfer FSGD file approach. Any help would be highly appreciated, 
Thanks!
___
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 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.