-parc_dir should really be "seg volume". It is the name in the mri dir of the volume that contains the manual labelings.

xform we use to put it in Tal coords. We also usually iterate where we build an initial atlas, then align all the volumes to it and rebuild, but if you have talairach.m3z you can just use it. And yes, you can use the T1 and T2 mprages if you want (I would intensity normalize them first)

cheers
Bruce




On Mon, 4 Jun 2018, arsene ella wrote:

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Hi Bruce,
Thanks for your promt answer... but what about the others questions? I mean :

  -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?

Cheers,

Arsene


2018-06-04 21:32 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Arselle

      the node_spacing is the mm resolution of the atlas Markov priors and class-conditional densities, the
      prior_spacing is the same for the classwise spatial priors

      the equivalent for the surface is mris_ca_train. It takes annot files as input

      cheers
      Bruce

      On Mon, 4 Jun 2018, arsene ella wrote:


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            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


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