One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ...
Otherwise, you can run fscalc, eg,

fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o mgx.ctxgm.rescaled.nii.gz



On 11/20/2020 11:44 AM, Boris Rauchmann wrote:

        External Email - Use Caution        

Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean intensity using PETSufer? Is there a command to use in mri_gtmpvc like --rescale X? 
I know that I can find the mean in  global.gm.dat and I can use that value for scaling the atlas based results in gtm.stats.dat but how can I easily scale the image?

Thanks, 
Boris


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer