Hi Fred

can you explain what " cortical thickness volumetric data in MNI space" means? Thickness is not a volumetric quantity - it is undefined for much of the volume (the part that is not in cortex). You could sample the thickness into the ribbon, but what you would find is that the individual subject ribbons don't line up in MNI space

cheers Bruce

On Wed, 11 Jun 2014, Fred Sampedro wrote:

Hi again,

Any suggestions at least conceptual to the path I should follow to obtain cortical thickness volumetric data in MNI space?

Thanks!

On Sun, Jun 8, 2014 at 6:54 PM, Fred Sampedro fredsampedro@gmail.com wrote: Dear FreeSurfer experts,

  I am interested in analyzing group differences in cortical
  thickness with an application-specific GLM model that is build
  to work on MNI152 volume data.
  For that, my plan is to obtain a "cortical thickness volume in
  MNI152 space" for each of my MRI scans. My input data are nifti
  T1 scans. Here is my pipeline proposal for each T1 scan:

  INPUT: FOO_SUBJECT.nii

  FREESURFER CALLS (in $SUBJECTS_DIR):
      1) recon-all -i FOO_SUBJECT.nii -subjid foosub
      2) recon-all -all -subjid foosub
      3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o
  foosub_cth_vol_lh  #(?)
      4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o
  foosub_cth_vol_rh  #(?)
      5) #should I merge lh and rh (?) how (?) let it be
  foosub_cth_vol
      6) fslregister --s foosub_cth_vol --mov
  /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat 
  #should I convert it to MNI152 space (?) and how (?)
      6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol #
  should I smooth it (?) and how (?)
     
  OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?)

  As you can see, I am pretty new to freesurfer and I have a lot
  of technical and conceptual gaps in this pipeline.

  Any advice on how to robustly accomplish this task would be much
  appreciated, as well as any advice regarding whether it would be
  a bad idea to try to carry out this kind of procedure in the
  first place. The context of the application is to apply the same
  ad-hoc statistical groupal analysis to PET, VBM GM, and cortical
  thickness data for all subjects.

Thanks a lot in advance, Fred Sampedro