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#acl WikiUserGroup:read,write,delete,revert All: = Buckner40 Notes = ''see also: Buckner40Testing and NewBuckner40Notes, Buckner40NotesCombined'' The 40 subjects in the [[FsTutorial/Data|buckner_data/group_study tutorial distribution]] have each been inspected for defects (by Jenni Pacheco, Evelina Busa, and Brian Quinn). These notes, combined with using tkmedit and tksurfer to observe the defects, serve as a good tutorial on what is considered 'good' and 'bad' output. Note: Some of these subjects are used as the example cases in the Morphometry and Reconstruction tutorial (specifically, subjects 008, 039, 095, 108, and 111). ||'''No.'''|| '''Inspection notes'''|| || || (first run 9/19/2005)|| || || (second run 9/29/2005, notes marked with *) || || || (third run 10/26/2005, notes marked with @) || ||004 ||LH temp lobe surfaces aren't good (coronal slice 116)|| || ||*surfs - ok|| || ||*aseg - hippocampus overlabeled in LH. RH lateral ventricle not labeled far enough posteriorly, in fact labeled as NONE. (subsequently not filled in wm.mgz but did not affect surface)|| || ||@surfs - temporal lobe wm not included in surface, but labeled in aseg - slice 128.|| || ||@asegs - bit of frontal lobe labeled as none (105 127 182)|| ||008 ||LH white surf in lateral vent not good (coronal slice 67)|| || ||RH pial surf misses a lot of temp lobe (slice 147)|| || ||*surfs - missing some of temporal lobe (both pial and white surfaces) RH coronal slice 145.|| || ||*surfs - basal ganglian defect not filled completely (sag. slice 157) creates a hole in the surfaces.(where the aseg labels Left-vessel and Right-vessel remains unfilled).|| || ||*aseg - accurately labeled the section of temporal lobe that is left out of the surface.|| || ||*aseg - some very posterior occipital lobe is left unlabeled (coords 103 180 52)|| || ||*aseg - ventricles not filled all the way posteriorly, and thus not filled in wm.mgz, but this did not affect the surfaces.|| ||017 ||LH surfs in lateral vent not good (coronal slice 49)|| || ||*surfs - ventricles not filled all the way posteriorly, affecting surface (cor slice 49)|| || ||*aseg - ventricles not labeled all the way posteriorly.|| || ||*aseg - both hippocampi seem overlabeled|| || ||@surfs - temporal lobe left out of wm coords 155 141 105|| ||021 ||LH artery is little island of pial surface (coronal slice 139)|| || ||*surfs - ok|| || ||*aseg - ok|| ||032 ||not bad overall (pial in frontal lobes could extend a bit)|| || ||*surfs - basal ganglian defect not filled completely (cor slice 129) creates a hole in the surfaces.(where the aseg labels Left-vessel and Right-vessel remains unfilled)|| || ||*aseg - ventricle labeled wrong coord 105 127 75|| ||039 ||bad talairach alignment|| || ||*surfs - cutting planes are off.|| || ||*aseg - RH/LH boarder is correct here.|| ||040 ||LH pial surf a bit tangled (slice 92 - vol index 145 142 92)|| || ||*surfs - ok|| || ||*aseg - ok|| ||045 ||superior CC cut plane too much in LH|| || ||RH pial sur misses a lot of temp lobe (slice 139)|| || ||LH pial sur misses a lot of frontal & temp lobe (slice 146)|| || ||*surfs - cutting planes off|| || ||*aseg - ok|| || ||@surfs - temporal lobes better, but still not great. 89 129 141 || || ||@surfs - temporal lobe WORSE here 156 145 116 and 104 145 123 misses entire strand|| ||049 ||not bad overall|| || ||*surfs - ok|| || ||*aseg - ok|| ||067 ||good overall|| || ||*surfs - a bit of temp lobe excluded in COR slice 139 ish.|| || ||*aseg - some labeling as none near ventricles coords 148 102 145 and 112 161 50 (causing the ventricles to be left unfilled but not affecting the surfaces in that area)|| || ||@surfs - i think it's better, but there is still some temporal lobe left out in slice 139 ish. 86 136 139 || ||073 ||good overall|| || ||*surfs - basal ganglian defect not filled completely coords 96 137 129 creates a hole in the surfaces.(where the aseg labels Left-vessel and Right-vessel remains unfilled)|| || ||*surfs - pial surfaces include some non-grey matter in slices 158 and up.|| || ||*aseg - ok|| || ||@surfs - problem with white surface here 153 156 128 and here 93 143 129, leaving holes in surface|| ||074 ||temp lobes - lose some pial and white surfs (slice 147)|| || ||*surfs - basal ganglian defect not filled completely coords 99 118 128 creates a hole in the surfaces.(where the aseg labels Left-vessel and Right-vessel remains unfilled)|| || ||*surfs - portion of temp lobe excluded coords 79 119 138|| || ||*aseg - portion of temp lobe excluded from surfaces is accurately labeled in aseg.|| ||080 ||very bad, most of inferior brain surfs are missing|| || ||*surfs - temporal lobes horrible. excluded from surfaces AND asegs. Intensity is correct, 110. checked tal in tkregister2, looks ok.|| || ||*aseg - temporal lobes horrible. excluded from surfaces AND asegs|| || ||@surfs - same as before - talairach may be the culprit|| ||084 ||good overall|| || ||*surfs - portion of temporal lobe excluded coords 101 158 128. control points maybe|| || ||*aseg - portion of missing temporal lobe is accurately labeled in aseg|| || ||@surfs - temporal lobe being excluded 102 158 128|| ||091 ||not bad overall|| || ||*surfs - ok|| || ||*aseg - ok|| ||092 ||good overall|| || ||*surfs - ok|| || ||*aseg - ok|| ||093 ||good overall|| || ||*surfs - ok|| || ||*aseg - ok|| ||095 ||very bad - CC plane in medial LH, pial surf in RH not good (slice 68)|| || ||*surfs - large portions of RH temporal lobe excludes|| || ||*surfs - cutting planes HORRIBLE. bad talairach. || || ||*aseg - ok|| || ||@surfs - problem here 154 110 125, mislabeled as cortex in aseg as well, talairach still bad. all other problems fixed!!|| ||097 ||RH temp lobe loses pial (slice 146), LH pial wonky laterally (166)|| || ||*surfs - basal ganglian defect not filled completely coords 103 139 127 creates a hole in the surfaces.(where the aseg labels Left-vessel and Right-vessel remains unfilled)|| || ||*aseg - ok|| || ||@surfs - pial still cuts off some temporal lobe, RH starting around COR slice 142|| ||099 ||RH frontal lobe surfs on slice 150? (132 165 150) otherwise good|| || ||*surfs - ok|| || ||*aseg - ok|| ||102 ||good overall|| || ||*surfs - LH frontal lobe pial gyri cut off (e.g. coronal slice 169, V.I.135 120 169) also pial surfs are fragmented in coronal slice 189 white surfs loook bad in coronal slice 90 -- LH lat vent and RH gyrus|| || ||*aseg - coronal slice 126 -- way too much subcortical stuff excluded,e.g. RH amygdala, hyippocampus... || ||103 ||a chunk of RH artery in pial surface (slice 145) otherwise good|| || ||*surfs - cor slice 146 - RH crud included in pial surf 111 132 146|| || ||*aseg - reasonable || || ||@surfs - RH artery still included 111 133 146 || ||106 ||good overall|| || ||*surfs - RH temp lobe not good - coronal slice 138 -79 128 138 /medial LH not good 128 122 157, LH frontal lobe gyrus misses a lot - 137 137 181|| || ||*aseg - a few NONE voxels in the lateral vents, a lot of non-brain crud labelled as cerebral cortex 68 101 92|| ||108 ||very bad -- RH cereb missing, RH temp lobes losing surfs (145)|| || ||inferior RH occip lobe labeled as cereb cortex in aseg 95 146 87|| || ||*surfs - RH lateral temp lobe misses out as usual 81 129 151, and pial is tangled here --> 72 134 129|| || ||*aseg -129 120 166 non-brain crud labelled as WM || || ||* * * RIGHT HALF OF CEREBELLUM MISSING|| || ||@surfs - RH cerebellum is missing still|| ||111 ||temporal lobe: disconnection of thin gyri, slices 133-135|| || ||frontal lobe: misclassification of non-wm as wm, slice 179+-10|| || ||lateral ventricle: not filled, slice 50-168|| || ||*surfs - some skull picked up as pial coronal slice 50, LH temp lobe sucks 166 142 160|| || ||*aseg - pretty bad, check LH lateral vent for e.g. 146 144 51/some skull labelled as cortex coronal slice 50, lots of crud labelled as cortex - 77 131 160/ quite a few NONE voxels - 107 103 160|| || ||* * * BOTTOM HALF OF CEREBELLUM STRIPPED|| || ||@surfs - better than before. cerebellum still stripped at bottom|| ||114 ||not very good - overall loss of outer pial surface|| || ||*surfs - lots of stuff excluded -- look at coronal slice 155 -- LH frontal occipital gyri, weirdness in RH temp lobe, 99 71 135 <--this entire area (superior lateral frontal RH is excluded from pial surfs)|| || ||*surfs - large portion of corpus callosum left out (125 116 88) normalization problem|| || ||*aseg - labeling as none around the ventricles (145 94 144) and here (108 122 95)|| || ||*aseg - lots of wm labeled as cortex in COR slice 52|| || ||@surfs - pial surf misses a lot of cortex here 99 74 128 - lots of problems like this throughout|| ||123 ||not bad overall|| || ||*surfs - not bad, RH temp lobe surfs fragemented again (cor slice 144) also weirdness labelled as pial 132 148 136|| || ||*aseg - too many NONE voxels around lateral vents e.g. cor slice 88|| ||124 ||good overall|| || ||*surfs - okay, a bit of pial tangling at 111 114 137, lateral RH temp lobe cuts out e.g. coronal slice 140|| || ||*aseg - seems ok || ||128 ||not bad overall|| || ||*surfs - ok|| || ||*aseg - labeling as none around ventricles (109 105 143)|| || ||*aseg - poorly labeled wm (labeled as cortex) see SAG slice 118|| ||129 ||not bad overall|| || ||*surfs - 114 117 157 RH blob, 128 111 171 RH gyrus intersect/fragment|| || ||*aseg - ok, a lot of post-occipital skull labeled as cortex, vessel/ganglia causing surf probs 159 105 136|| || ||* * * * LH INFERIOR CEREBELLUM STRIPPED (see coronal slice 90)|| ||130 ||good overall|| || ||*surfs - pretty good, but some pial tangling in LH 183 133 78|| || ||*aseg - lateral vents called hypointensities sometimes... 157 117 78 but look okay in horizontal plane, but also labelled as NONE sometimes! 107 116 61 RH - coronal slice 61|| ||131 ||good overall|| || ||*surfs - ok - some vessels in pial surface.|| || ||*aseg - labeling as none around ventricles.|| || ||*aseg - skull labeled as cortex see COR slice 157|| ||133 ||not bad overall|| || ||*surfs - ok|| || ||*aseg - labeling as none around ventricles|| || ||*aseg - mislabeled wm (111 87 63)|| ||136 ||good overall|| || ||*surfs - ok|| || ||*aseg - labeling as none around ventricles|| ||138 ||not bad overall|| || ||*surfs - some pial tangling and wm of temp. lobe goes and comes back 102 142 126|| || ||*aseg - labeling as none around ventricles|| ||140 ||good overall|| || ||*surfs - ok|| || ||*aseg - lots of voxels labeled none 104 102 102 and 152 100 102|| ||141 ||good overall|| || ||*surfs - ok|| || ||*aseg - wm mislabeled as cortex 146 30 111|| ||144 ||very bad - CC cutting plane in medial RH, LH lat ventr surfs not good,|| || ||artifacts in scan (e.g. slice 125)|| || ||*surfs -cutting planes are awful - talairach bad|| || ||*aseg - not great. RH/LH boarder accurate in aseg. || ||145 ||bad seg - orbital fat labeled as RH wm (slice 173), L/RH temp lobe, surfs 143|| || ||*surfs - ok|| || ||*aseg - eh, ok i guess.|| ||149 ||not bad overall|| || ||*surfs - ok|| || ||*aseg - labeling bad through occip. lobe SAG slice 146|| |
- Diff for "Buckner40Notes"