
cvs_age35_inMNI152/mri.2mm

These are volumes sampled into the 2mm space of the MNI152. The
primary purpose of these is to support volume-based fMRI analysis as
performed in FS-FAST.

These files can be used to render the statistical results on a volume
(though this is not really necessary as they can be rendered directly
on the 1mm volumes). Also, the aseg.mgz created can be used to
generate labels/masks of subcortical structures directly in the group
average space. These can be used with mri_volcluster.

These files were created with the following commands:

# Create a registration to the MNI152 2mm space

tkregister2  --s cvs_avg35_inMNI152 --regheader --reg register.dat \
  --ltaout register.lta --noedit \
  --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz

# Resample each of these volumes using trilin
foreach vol (orig brain brainmask nu T1)
  mri_vol2vol --targ ../mri/$vol.mgz --reg register.lta \
   --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz \
   --o $vol.mgz --inv
end

# Resample the aseg 
mri_label2vol --seg ../mri/aseg.mgz --temp orig.mgz \
  --regheader ../mri/orig.mgz --o aseg.mgz

Note: we don't want to do aparc+aseg because the surface-based 
labels should really be used in a surface-based analysis.

# checks
tkmedit -f T1.mgz -aux brain.mgz -seg ./aseg.mgz
tkregister2 --mov ./orig.mgz --s fsaverage --regheader --reg junk

#-----------------------------------------------------------

Creation of subcortical mask. Since this is CVS space, we will
asume that the subcortical structures in the ASEG are sufficient.
Dilate by 1 to make sure.

8   Left-Cerebellum-Cortex  
10  Left-Thalamus-Proper    
11  Left-Caudate            
12  Left-Putamen            
13  Left-Pallidum           
16  Brain-Stem              
17  Left-Hippocampus        
18  Left-Amygdala           
26  Left-Accumbens-area     

47  Right-Cerebellum-Cortex 
49  Right-Thalamus-Proper   
50  Right-Caudate           
51  Right-Putamen           
52  Right-Pallidum          
53  Right-Hippocampus       
54  Right-Amygdala          
58  Right-Accumbens-area    


mri_binarize --match 8 10 11 12 13 16 17 18 26 47 49 50 51 52 53 54 58 \
  --i aseg.mgz  --dilate 1 --o subcort.mask.mgz

