Hi- Just gently re-bumping this question/thread.
Noting that the previous thread with recommendations about non-GM ROIs, which I used in the coming up with the GM list above, is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50005.html Thanks, pt On Mon, Dec 12, 2016 at 10:43 AM, P Taylor <neon.tay...@gmail.com> wrote: > And, a minor clarification on one of the ROIs in question-- > > I should have phrase the comment about ROI #80 as follows: > 80 non-WM-hypointensities -------> *should be in list of FS_nongm? > > ... since the name clearly implies that it is non-WM. > > Basically, I am first wanting to check that the above list of ROIs does > form the "whole brain" returned by recon-all; there are a lot more ROIs > listed in the LUT, of all sorts of tissue types, but it seems like those > don't often appear in the output. > > And following on that, it seems like presently a map of various non-GM > tissues is made by summing up ROIs of a given type, and then: > GM_map = whole_brain - WM_map - CSF_map - vent_map. > However, am I interpreting things correctly that the four ROIs flagged > above (#30, 62, 80 and 85) seem to be an "other" class that should be > subtracted away from the whole_brain, as well, such that: > GM_map = whole_brain - WM_map - CSF_map - vent_map - other_four_regions ? > > Thanks, > pt > > > > On Mon, Dec 12, 2016 at 1:04 AM, P Taylor <neon.tay...@gmail.com> wrote: > >> 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 >> > >
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