The ICV is calculated during the -segstats step with all of the other
volume measures that use the aseg. They are all found within the
aseg.stats file in the stats subdir.
Jenni
On Mon, 24 Jul 2006, Graham Wideman wrote:
Folks:
A couple of weeks ago, Bruce noted that:
EM Registration with Skull is for generating ICV measures
... so I just got around to investigating where the ICV measures might be
getting saved.
Bottom line is I don't see what file that ICV measure is getting saved into.
Details:
I tried to figure out which program/script does this step, and what files it
produces which might capture ICV.
1. Which commands correspond to the "EM Registration with Skull" step? Clue:
wiki recon-all shows this step employs the <no>skull-lta step. Looking in
recon-all script, this corresponds to the DoSkullLTA variable, and that in
turn leads us to mri_em_register as the pertinent command.
2. Looking at docs for mri_em_register in the wiki shows 4 arguments, only
one of which is flagged. Looking at actual help output from mri_em_register
shows about 50 flagged arguments, none described.
3. The pertinent bit of script looks like this:
set xopts = `fsr-getxopts mri_em_register $XOptsFile`;
set cmd = (mri_em_register -skull -t transforms/talairach.lta \
$xopts nu_noneck.mgz $FREESURFER_HOME/average/$GCASkull \
transforms/talairach_with_skull.lta)
4. From all this, I don't see what output file mri_em_register might be
placing the ICV into.
Clues?
Thanks,
Graham
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