[MINC-users] Volumetry and Talairach boxes

[D. Louis Collins]

Ed,

This should not be difficult, although no one-line command exists to do 
what you need.  I suggest the following, starting with a subj,mnc in 
native (scanner) space.

mritotal subj.mnc subj_to_tal.xfm
mincresample subj.mnc subj_tal.mnc -transformation subj_to_tal.xfm 
-like icbm_template_1.00mm.mnc
classify_clean subj_tal.mnc subj_classes.mnc

you'll need a method to strip the skull to create a brain mask.  We use 
minc_bet, a derivative of BET from FSL.

minccalc -expression 'A[0]>0.5? A[1] : 0' subj_brain_mask.mnc 
subj_classes.mnc subj_brain_classes.mnc

now the fun part.  You'll need to chop up the brain into the twelve 
Talairach boxes and then use print_all_labels to get the volume of each 
tissue in each box.  For example, to get the right frontal superior 
block:

mincreshape -dimrange zspace=72,85 -dimrange xspace=90,70 -dimrange 
yspace=126,80 \
    subj_brain_classes.mnc block.mnc

you'll need to play with the start and extent voxel indexes to get each 
of the twelve blocks correctly defined.

to get the volume of tissue for each block:
print_all_labels block.mnc

hope this helps,

-Louis



On Jan 3, 2006, at 7:34 AM, Ed Gronenschild wrote:

> Hi all,
>
> First of all, I wish everyone a happy new year.
>
> I was wondering if it is possible with the MNI software to perform
> volumetric
> measurements of gray and white matter and liquor for the whole brain 
> and
> within Talairach boxes.
>
> Kind regards,
>
> Ed
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>