Hi, Doug-
I've looked more into my earlier question of identifying FS-returned regions, in particular: 1) which regions of the whole FreeSurferColorLUT.txt seem to get returned by default recon-all calls (for either the 2000- or 2009-parc+segs); and 2) which of those regions are GM and non-GM (WM/CSF/other), based both on the mri_binarize list you had posted earlier in this thread and on the names given in the LUT.
I'd like to pick your brain on this.
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.
C) For the ROIs specific to 2009aparc+aseg, I think it also seems pretty clear: + 11100 and 12100 are returned as "ctx_*_Unknown"; + All ROIs in the intervals [11101, 11141] and [11143, 11175] can be returned, and these are all LH GM; + All ROIs in the intervals [12101, 12141] and [12143, 12175] can be returned, and these are all RH GM; + ROIs '11142' and '12142' are the "ctx_?h_Medial_wall", which would be non-GM, 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