Hello FreeSurfer users/devs,

I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct?

1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume —tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume file to .mgh file)

2) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume --mean --fwhm 0 --o $PWD/$h.volume.pop_mean.mgh (obtain mean population volume at each vertex)

3)  mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume —std --fwhm 0 --o $PWD/$h.volume.pop_std.mgh (obtain volume standard deviation volume at each vertex)

4) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_mean.mgh —tval $sub/surf/$h.volume.pop_mean.mgh —hemi $h (map population mean to subject space)

5) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_std.mgh —tval $sub/surf/$h.volume.pop_std.mgh —hemi $h (map population std to subject space)

6) fscalc $sub/surf/$h.volume.mgh sub $sub/surf/$h.volume.pop_mean.mgh div $sub/surf/$h.volume.pop_std.mgh -o $sub/surf/$h.volume_z.mgh

7) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume_z.mgh —tval $sub/surf/$h.volume_z —tfmt curv (convert .mgh to curv file)

After z-scoring each vertex, I want to do a group analysis between the two groups in my cohort. Instead of using raw volume as my measurement, I would be using z-scored volume.

Thanks for the help,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

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