Subjid

Versions & Notes

Stable 5.2*

Stable 5.1*

Stable 5.0*

Stable 4.3**

Older unknown version***

run: 04/22/2013

run: May 3, 2011

run: October 18, 2010

run: 12/30/2008

run1: 9/19/2005

run2: 9/29/2005

run3: 10/26/2005

004

-Ventricle needs to be filled in around coords 124 114 110 to correct the surfs in that area
-WM lesions in few areas

-tologolical defect 138 138 184, 127 142 161
-surfs not go all the way in to ventricle 102 125 67buckn

-gm counted as wm at coords 113 140 147
-dura mistaken as wm 115 143 162

-pial surface excluding some grey matter at coords 92 125 127
-dura labelled as grey matter at coords 81 151 153

-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

-WM lesions at 112 74 127, 137 86 124, 161 115 58, 107 72 112, 132 71 112, 156 102 158

-ran skullstrip again to get rid of extra dura (ran w/ gcut)
-calcarine labeled as ventricle 150 149 72

-skulstrip error - part of the cerebellum is missing
-wm mistaken as gm creating a pial surf where it shouldn't be (155 134 134)
-pial surf cutting into wm surf (78 136 68 & 117 79 117)
-dura mistaken as wm (110 132 164)

-wm lesion at coords 109 98 162
-lateral ventricles not filled in or WM lesion at coords 100 150 69 ?
-erratic pial surface at coords 108 97 159, 82 97 110, 106 81 110

-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.

N/A

017

-Needs some minor WM edits. Otherwise looks okay

-topological defect 138 138 176, 134 140 160

-surfs cutting into lateral ventricles (~65)
-dura interfering with pial surf (95 135 141)

-WM and pial surfaces include dura starting from coronal slice 160 at coords 112 143 160 and upto slice 144
-topological defect at coords 139 141 165 ?
-Pial surface cutting into cerebellum 114 149 57
-Erratic WM and pial surfaces 110 128 49

-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

Looks okay overall

-toptological defect 139 122 164

-surfs cutting into the lh lateral ventricle (slice ~66) -surfs not going all the way in on both sulci (slice ~98)

-grey matter labelled as WM at 170 155 114. Aseg looks okay at these coords though
-pial surface not extending all the way in left inferior lateral ventricle at 161 140 97
-white matter and pial surfaces cutting into left lateral ventricle at 157 142 67

-LH artery is little island of pial surface (coronal slice 139)

-surfs - ok
-aseg - ok

N/A

032

-WM lesions at coords 137 67 149, 134 62 137, 88 75 124
-surfaces look off at the posterior portion of left lateral ventricle at coordinates 154 135 68, 105 133 69

-low intensity wm 139 124 145
-calcarine labeled as ventricle 155 135 65, 105 129 73

-surfs on both sulci not going all the way in (fs confusing it with lat. ventr. - slice ~60)
-surfs are weird near lateral ventricles (slice ~90)

-Not sure if this area is calcarine or lateral ventricle at 155 131 70. Error occurs in both the hemispheres

-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

N/A

039

-WM lesions at coordinates 133 93 107, 113 95 105
-Surfs off at the posterior portion of left and right lateral ventricle

-topological defect 132 153 146, 124 151 156, 132 161 56
-calcarine labeled as ventricle 151 158 74

-surfs are weird around the ventricles (slice ~78)
-wm not included in the surfs (coords 122 147 145 & 133 160 65)
-dura taken as wm (114 155 153)
-pial surf cutting into wm surf (134 151 145)

-Topological defects at 131 161 57, 124 151 154
-Not sure if this area is calcarine or lateral ventricle at 151 159 72

-bad talairach alignment

-surfs - cutting planes are off.
-aseg - RH/LH boarder is correct here.

N/A

040

-white surface cutting into lateral ventricle at 103 137 82

-topological defect 140 137 166, 127 133 156
-surfs going into inf lat vent ~104

-dura taken as wm (95 139 147)
-wm or dura?? (140 137 168)

N/A

-LH pial surf a bit tangled (slice 92 - vol index 145 142 92)

-surfs - ok
-aseg - ok

N/A

045

-white surface excluding some WM in left temporal lobe
-Surfs off near posterior portion of left and right lateral ventricle

-intensity problem on lh temp lobe ~151
-calcarine labeled as ventricle 154 138 64
-surfs overlap at ventricle 106 138 73

-surfs are messed up around the ventricles (~60)
-surfs not including wm (96 149 112 & 84 153 99)

-topological defect at 160 150 140 ?
-Not sure if this area is calcarine or lateral ventricle 153 139 62
-topological defect at 96 148 112

-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

-pial surface crossing white surface around coordinates 158 119 75

-topological defect (low intensity) 14 128 168

-dura taken as wm (120 132 70 & 176 104 100)
-pial surf cutting into wm surf (104 153 142)
wm surf loop (187 93 98 & 84 104 118)

N/A

-not bad overall

-surfs - ok
-aseg - ok

N/A

067

-surfs look slightly off at posterior portion of left lateral ventricle

-topological defect tip of temp lobes ~138, and 124 120 166
-extra skull left in posterior - cortex overlabeled

-lat. ventricles surfs are messed up (~44 & ~65)
-gm taken as wm (122 135 140)

-white matter and pial surfaces cutting into ventricles at 148 159 42 ?

-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

-surfs look off at posterior portion of left and right lateral ventricles

-calcarine labeled as ventricle 159 136 79 making surfs overlap

-lat. ventricles area surfs are messed up (~76)

-Not sure if this area is calcarine or lateral ventricle 102 141 61

-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

-WM lesions messing up surfaces around coordinates 139 57 108, 119 58 108
-Surfs off at posterior portion of left and right lateral ventricles

-topological defects 128 119 161 & on temporal lobes (low intensity) ~150
-intensity problem (147>110) 141 131 41
-calcarine labeled as ventricle 155 133 7
-extra dura around temp lobes and posterior making cortex overlabeled

-calcarine mistaken as lat. ventricle

-Not sure if this area is calcarine or lateral ventricle 155 132 74

-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.

N/A

080

-Looks okay overall

N/A

N/A

-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

-bright spot around coordinates 140 155 51 is messing up the surfaces slightly around that area

-topological defect (low intensity) 147 133 153,148 149 128

-wm not included in surfs (178 157 119)
-pial surf cutting into wm surf (152 147 88 & 75 104 104)
-dura taken as wm (117 134 167)

-pial surfaces crossing over WM surface at coords 94 81 149, 132 123 146
-WM surface excluding WM -pial surface tangled in all the views (Cor, Sag, Hor) at 139 137 130
-pial surface tangled at coords 134 122 147 in coronal view, but looks okay in other views, which is fine

-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

-surfs slightly off at posterior portion of right lateral ventricle
-Pial surface crossing white near left lateral ventricle

topological defect (intensity) 141 133 167
-cortex over labeled to cerebellum 141 159 45
-cerebellum aseg missing 133 166 45

-pial surf cutting into wm surf (133 127 177)
-lat. vent. area (95 146 109)
-gm taken as wm (94 125 170)
-ventr. mistaken as calcarine (128 128 71)

N/A

-not bad overall

-surfs - ok
-aseg - ok

N/A

092

-few WM lesions. Otherwise looks okay

-topological defect 134 137 181

-skullstrip error - part of the cerebellum is missing
-dura taken as wm (114 141 166, 170 119 135, 112 139 165 & 174 130 140)

N/A

-good overall

-surfs - ok
-aseg - ok

N/A

093

Ventricle needs to be filled in wm.mgz at 133 123 137

topological defect 125 133 177

-pial surf cutting into wm surf (167 142 149 & 81 132 138)
-loop of wm surf (124 102 181)

-pial surface curves sharply inwards and also crosses WM surface at coords 133 123 135
-pial and main surface curve inward again at coords 133 111 117

-good overall

-surfs - ok
-aseg - ok

N/A

095

-surfs off around coordinates 88 110 138, 171 107 138
-WM lesions in quite a few areas
-Surfs slightly off near posterior lateral ventricle of both hemis

-surfs going in through wm 161 111 128, 87 114 129
ventricle labeled as sulcus 149 163 60

-**skullstrip failure** no cerebellum and part of the cortex is labeled as the cerebellum - really bad! - fixed with watershed method
-surfs around calcarine area are messed up (111 162 62)
-surf not including wm (107 175 72)

-tangled WM and pial surfaces. pial surface crosses over the WM surf. WM surf does not include some of the WM at coords 168 110 139
-pial surface curves sharply inwards at coords 158 123 138, 131 132 131
-WM segmented as grey matter at coords 141 88 102

-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

-looks okay overall

-topological defect (low intensity) 85 142 148
-extra dura posterior making cortex overlabeled

-dura taken as wm (117 147 153)
-pial surf cutting into wm surf (79 139 140)

-topological defect at coords 88 144 153. WM mislabelled as grey matter in aseg
-topological defect at coords 177 111 153. WM mislabelled as grey matter in aseg

-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

-surfs off around posterior portion of right lateral ventricle

-calcarine labeled as ventricle 150 143 83
-wm labeled as gm making surfs messed up near ventricle 93 141 69

-lat. vent. area surfs
-pial surf cutting into wm surf (94 94 145)

-topological defect at coords 132 158 57
-Pial surface cutting into Cerebellum at coords 114 161 60

-RH frontal lobe surfs on slice 150? (132 165 150) otherwise good

-surfs - ok
-aseg - ok

N/A

102

-surfs need to be corrected around coordinates 110 59 127

-lat. vent. area
-dura taken as wm (113 123 163 & ~170)

N/A

-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...

N/A

103

-few WM lesions. Otherwise looks okay

-dura taken as wm (175 120 133)
-pial surf cutting into wm surf (78 93 78)

N/A

-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

-surfs off around posterior portion of right lateral ventricle

-ventricle labeled as cortex messing up surfs 103 121 78
-extra dura in posterior making cortex overlabeled

-ventricle mistaken as calcarine (102 118 76)
-gm included as wm (123 142 159)
-pial surf cutting into wm surf (123 131 193)

-pial surface crosses over WM surface at coords 113 121 97

-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

N/A

108

-ventricle probably needs to be filled in to correct the surfs around coords 132 126 142
-Surfs slightly off around posterior portion of right lateral ventricle

-low intensity problem 138 144 178, 133 143 156

-dura taken as wm (84 121 139, 185 119 133, 170 150 109, 82 156 120 & 143 137 108)
-ventricle?? (152 124 65)

-pial surface tangled at coords 83 136 149, 160 154 160 in all the views
-pial surface is excluding some brain tissue. Not sure if it's a lesion. coords are 105 127 65. Needs WM edits?
-in aseg, dura is labelled as grey matter at coords 124 78 56

-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

-looks okay overall

-cortex overlabeled to eyeba-very bright - poor contrast b/t gm and wm

-skullstrip errror - more of lh cerebellum is stripped off
-dura taken as wm (115 139 166)
-lh lateral ventricle area (~55)

-pial surface crossing over WM surface at coords 80 86 128
-pial surface curves inward sharply at coords 132 128 145

-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

-brainmask.mgz looks pixellated causing low WM intensity in many areas (mainly posterior). This is messing up the surfaces

-surfs going into ventricles ~72
-topological defect due to low intensity 88 146 129, 103 144 141, 155 135 148, 135 117 154, 90 80 139 - and large part of the posterior
-surfs around ventricle messed up 146 147 57

-skullstrip error - a little bit of cerebellum is stripped off toward posterior
-really bad case overall
-mesh of pial surf (119 65 101 &17 150 82)
dura taken as wm (93 162 69 & 117 120 155)
-lh lateral ventricle not filled in all the way (~65)
-pial surf cutting into white surf (92 148 86 & 120 118 143)
-rh ventricle not filled in (~68)

-topological defect at 101 74 136
-pial surface crossing over WM surface at 97 91 160

-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

looks okay overall

-pial surf messed up (143 144 106)
-gm taken as wm connecting temp. lobe gyrus to ventricle (134 131 97)

N/A

-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

N/A

124

-WM lesions in few areas
-Pial surface cutting in sharply at coords 112 98 78

-topological defect 139 127 170

N/A

-erratic pial surface at coords 139 69 178, 138 59 161
-lesion at coords 139 65 149, 138 53 144?

-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

N/A

128

-Pial surface cutting in sharply at coords 100 143 79, 157 147 73

-topological defect 125 128 148
-calcarine labeled as ventricle 148 150 66

-pial surf cutting into white surf (96 86 148 & 95 141 146)
wm not included in surf (141 156 53)

N/A

-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

N/A

129

-pial surface cutting in sharply at coords 111 112 73
-surfs off at posterior portion of left lateral ventricle

-topological defect 142 109 175
-surfs messed up at ventricle 160 104 80
-cortex overlabeled to dura posteriorly

-dura taken as wm (114 117 158)

N/A

-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)

N/A

130

-surfs off at posterior portion on both right and left lateral ventricle

-surfs going in ventricle 99 118 80

-dura taken as wm (92 120 135, 143 146 186 & 102 134 142)
-ventricle mistaken as calcarine (99 119 79)

N/A

-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

N/A

131

-looks okay overall

-topological defect 135 104 147, 82 105 147
-cortex overlabeled to dura posteriorly

-skullstrip error - tiny bit of lh cerebellum is missing

N/A

-good overall

-surfs - ok - some vessels in pial surface.
-aseg - labeling as none around ventricles.
-aseg - skull labeled as cortex see COR slice 157

N/A

133

-looks okay overall

-dura taken as wm (109 123 164)

N/A

-not bad overall

-surfs - ok
-aseg - labeling as none around ventricles
-aseg - mislabeled wm (111 87 63)

N/A

136

-surfs off around posterior portion of right and left lateral ventricles

-surfs weird at ventricles ~75

-skullstrip error - part of lh temporal lobe is stripped off - fixed by adjusting watershed threshold
-lateral ventricles area (~71)

N/A

-good overall

-surfs - ok
-aseg - labeling as none around ventricles

N/A

138

-pial and white surface curving in sharply around coords 133 105 128

-topological defect 124 124 146
-cortex overlabled to dura around lh temp lobe ~146

N/A

N/A

-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

N/A

140

-looks okay overall

-topological defect 14 122 157

-dura taken as wm (86 98 117 & 119 126 178)
-pial surf cutting into white surf (109 102 200)

N/A

-good overall

-surfs - ok
-aseg - lots of voxels labeled none 104 102 102 and 152 100 102

N/A

141

-WM lesions in few areas
-Surfs slightly off at posterior portion of right and left lateral ventricle

-topological defect 135 112 149
-ventricle mistaken as sulcus 107 86 75

-lateral ventricles area (~76)
-dura taken as wm (172 97 143)

N/A

-good overall

-surfs - ok
-aseg - wm mislabeled as cortex 146 30 111

N/A

144

-brainmask.mgz looks pixellated causing WM intensity to drop in some areas which in turn is causing some WM lesions

-low intensity area 140 109 185
-calcarine labeled as ventricle 147 141 83

-skullstrip error - a bit of lh cerebellum missing
-lateral ventricles area (~78)
-pial surf cutting into white surf (67 141 115)

N/A

-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.

N/A

145

-brainmask.mgz looks pixellated causing WM intensity to drop in some areas which in turn is causing some WM lesions
-Surfs off at posterior portion of right and left lateral ventricles

-topological defect tip of both temp lobes ~150
-calcarine labeled as ventricle ~70

-skullstrip error - part of the lh temporal lobe is stripped off - fixed by adjusting watershed threshold
lateral ventricles vs. calcarine area (~65)

N/A

-bad seg - orbital fat labeled as RH wm (slice 173), L/RH temp lobe, surfs 143

-surfs - ok
-aseg - eh, ok i guess.

N/A

149

-looks okay overall

-topological defect 122 133 172, 82 147 153, 169 178 97

-lh lateral ventricle area (~81)
-pial surf cutting into white surf (76 124 95, 117 130 178 & 97 114 178)
-dura taken as wm (113 144 164)

N/A

-not bad overall

-surfs - ok
-aseg - labeling bad through occip. lobe SAG slice 146

N/A

Subjid

Failure Modes

Segmentation Errors

Intensity Normalization

Pial Surface Misplacement

Skullstrip Errors

Topological Errors

004

x

x

x

x

008

x

x

x

x

x

017

x

x

021

x

x

032

x

039

x

x

x

x

040

x

x

045

x

049

x

x

x

067

x

x

073

x

074

x

080

x

084

x

x

x

091

x

x

x

092

x

x

x

x

093

x

x

x

095

x

x

x

x

097

x

x

x

099

x

x

102

x

x

103

x

x

106

x

x

x

x

108

x

111

x

x

x

114

x

x

x

x

x

123

x

x

124

x

128

x

x

129

x

130

x

x

131

x

x

x

133

x

x

x

136

x

x

138

140

x

x

x

141

x

144

x

x

x

x

145

x

x

149

x

x

Total

13

19

34

9

21