Hi, Doug-

A) The main questions I have relate to the regions labeled from [0, 256], which seem have the same labelling in both the 2000 and 2009 parc+segs.  From a few different FreeSurfer recon-alls on healthy adults, below is a list of the ROIs that seem to be consistently returned by recon-all (a much sparser subset than all 256).
For each, I have included the number and label, as well as put arrows by the numbers that, according to the MatchValues list in mri_binarize, should be in either the WM or Vent masks, (and hence non-arrowed regions should be GM, by how that function returns "--gm"). 
My main questions arise about #30, 62, 80 and 85, as they don't appear to be GM-- therefore, am I correct that I should also *exclude* those four regions from a list of GM regions?
(Here, "FS_nongm*" means that it was in the list of non-GM regions in mri_binarize, as either unknown, WM, CSF or ventricle.)

-----------------------------------------------------------------------------------------------------
  0 Unknown                       -> FS_nongm

  2 Left-Cerebral-White-Matter    -> FS_nongm_wm

  4 Left-Lateral-Ventricle        -> FS_nongm_vent
  5 Left-Inf-Lat-Vent             -> FS_nongm_vent

  7 Left-Cerebellum-White-Matter  -> FS_nongm_wm
  8 Left-Cerebellum-Cortex

 10 Left-Thalamus-Proper
 11 Left-Caudate
 12 Left-Putamen
 13 Left-Pallidum
 14 3rd-Ventricle                 -> FS_nongm_vent
 15 4th-Ventricle                 -> FS_nongm_vent
 16 Brain-Stem
 17 Left-Hippocampus
 18 Left-Amygdala

 24 CSF                           -> FS_nongm_csf

 26 Left-Accumbens-area

 28 Left-VentralDC

 30 Left-vessel                 -------> *should be in list of FS_nongm?
 31 Left-choroid-plexus           -> FS_nongm_vent

 41 Right-Cerebral-White-Matter   -> FS_nongm_wm

 43 Right-Lateral-Ventricle       -> FS_nongm_vent
 44 Right-Inf-Lat-Vent            -> FS_nongm_vent

 46 Right-Cerebellum-White-Matter -> FS_nongm_wm
 47 Right-Cerebellum-Cortex

 49 Right-Thalamus-Proper
 50 Right-Caudate

 52 Right-Pallidum
 53 Right-Hippocampus
 54 Right-Amygdala

 58 Right-Accumbens-area

 60 Right-VentralDC

 62 Right-vessel                -------> *should be in list of FS_nongm?
 63 Right-choroid-plexus          -> FS_nongm_vent

 72 5th-Ventricle                 -> FS_nongm_vent

 77 WM-hypointensities            -> FS_nongm_wm

 80 non-WM-hypointensities      -------> *should be in list of FS_nongm_wm?
 
 85 Optic-Chiasm                -------> *should be in list of FS_nongm?

251 CC_Posterior                  -> FS_nongm_wm
252 CC_Mid_Posterior              -> FS_nongm_wm
253 CC_Central                    -> FS_nongm_wm
254 CC_Mid_Anterior               -> FS_nongm_wm
255 CC_Anterior                   -> FS_nongm_wm
--------------------------------------------------------------------------------

It seem that the new version of mri_binarize that you had sent me might still include those four flagged regions in the 'mri_binarize --gm' output.

B) For the ROIs specific to the 2000aparc+aseg, I think it also seems pretty clear:
+ 1000 and 2000 are returned as "ctx_*_unknown";

+ All ROIs in the intervals [1001, 1003] and [1005, 1035] can be returned, and these are all LH GM;
+ All ROIs in the intervals [2001, 2003] and [2005, 2035] can be returned, and these are all RH GM;
+ ROIs '1004' and '2004' are the "ctx-?h-corpuscallosum", which would be WM, but they don't seem to be returned.


D) And you mentioned that the regions in the interval [3000, 4035] are WM parcellations.

So, in total, does that seem like a complete categorization of regions that are typically returned, as well as their classification as either GM or non-GM?  And in particular, I would be happy to know your thoughts on the flagged ROIs in the interval [0, 256].

Thanks,

pt