Hi Doug,

I have pasted the correspondences below. My question is, if I want to identify the PCs in a group for a single modality (PET), how should I run the mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance covariate)? 

Thanks !

Elijah 

Doug:

For within modality, you can add --pca to mri_glmfit (run it with --help 
to get more info). We do not have ICA tools in FS.

On 12/01/2016 02:04 PM, Foo Keat Mak wrote:
> Hi Freesurfer Team,
>
> For a given group, I want to look at the covariance patterns between 
> thickness and PET.  Within Freesurfer, what are some general workflow 
> tips on how I could go about performing PCA (within modality) or joint 
> ICA analyses looking at the covariance patterns across modalities?  Is 
> the -pca flag a good starting point?
>
> Any feedback is appreciated!
>
> Thanks a lot.
>
> Best Wishes,
> Elijah
>
>
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MGH-NMR Center
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