Gray Matter, White Matter or CSF Distributions at Cortex

The calculations of concentrations of one tissue type relative to other tissue types, on a point-by-point basis, at the cortical surface.

ucf_eat_volume* Converts a 3D model of the cortex into a 4D file with the gray matter density attached as a 4th parameter to the cortex. The gray matter map is supplied as a .mnc binary file. The resulting 4D maps can be used to measure patterns of gray matter distribution, loss, variability and asymmetry.

Example of Mapping Gray Matter Distribution: In this example, the greyonly clamped .mnc’s live in /data/scratch/people/greyimages/ and the elastically warped(reparameterized) cortical models live in the individual subjects’ directories /data/sampledatal/fas_sulcvar/analyze/control_flatmaps

The following code can be run in the csh:

  • set DIR=/data/sampledata/fas_sulcvar/analyze/control_flatmaps
  • foreach subject ( 1024 1101 1404 1524 1562 1597 1618 1973 2555 2783 2830 6533 6831 7746 7811 7863 8246 8684 8719 8785 8982 )
  • cd $DIR
  • cd ./{$subject}/CORT/WARP/
  • foreach x (*0*HEw*ucf)
  • /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/4D_UCFS/GRAY2/ucf_eat_volume 5 2 3 4 5 6 $x
  • /data/scratch/people/greyimages/{$subject}_avg_305_AIR1ord_greyonly_clamp.mnc.gz > grey_$x
  • end
  • cd $DIR
  • end

ucf_eat_volume_in_range** Same but this time the user specifies the intensity range of the MINC file, within which the attribute occurs, e.g. 0.5 1.5 (if the value is 1), rather than supplying the gray matter map is supplied as a .mnc binary file. Also the first parameter says how large a search radius to use (in mm, not voxels; e.g. 5, 10 or 15 are commonly used). The resulting 4D maps can be used to measure patterns of gray matter distribution, loss, variability and asymmetry.

*Program located in /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/4D_UCFS/GRAY2/ **Program located in /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/4D_UCFS/GRAY2/EAT_CLAMPED/