Dear All,

I have a set of 7 NIIFTI images (0.5 mm isotropic) :

- 2 average brain images (one T1W_MPRAGE and one T2W_SPACE template )

- 3 Tissue Probability Maps (Gray Matter, White Matter, CSF)

- 2 Atlases (One for Gray matter structures and another for Internal brain structures (or subcortical structures) ) segmented from mean images, labelled and annotated.

My question is: How to used these images to build Freesurfer-Like Atlases (.gca and .gcs) ?

For the .GCA, I don't really know what to set as Flagged Arguments...

mri_ca_train 
  -node_spacing 4 \                # ?
  -prior_spacing 2 \               # ?
  -parc_dir esegatlast \           # Is that the directory of my segmented subcortical structures?
  -xform talairach_one.m3d \       # All the files are aligned, so which transform shold I set here?
  -input flash30_avg.mgz \         # Should I set the T1W-MPRAGE average here? 
  -input flash5_avg.mgz \          # Should I set the T2W-SPACE average here?
  $SUBJECTS multi_one.gca

What about the .GCS?

Thanks in advance,

Arsene