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