''see also: Buckner40Adni60Testing, BugsInProgress, and AdniReconNotes''

'''Index''' <<TableOfContents>>

== Buckner40 Notes ==
||<tablewidth="1598px" tableheight="1336px"style="text-align: center;" |3>'''Subjid''' ||||||||||||<style="text-align: center; font-weight: bold;">Versions & Notes ||
||<style="font-weight: bold; text-align: center;">Stable 5.2* ||<style="font-weight: bold; text-align: center;">Stable 5.1* ||<style="text-align: center; font-weight: bold;">Stable 5.0* ||<style="text-align: center; font-weight: bold;">Stable 4.3** ||||||<style="text-align: center; font-weight: bold;">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 <<BR>>-WM lesions in few areas ||-tologolical defect 138 138 184, 127 142 161<<BR>>-surfs not go all the way in to ventricle 102 125 67buckn ||-gm counted as wm at coords 113 140 147<<BR>>-dura mistaken as wm 115 143 162 ||-pial surface excluding some grey matter at coords 92 125 127<<BR>>-dura labelled as grey matter at coords 81 151 153 ||-LH temp lobe surfaces aren't good (coronal slice 116) ||-surfs -  ok <<BR>>-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. <<BR>>-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)<<BR>>-calcarine labeled as ventricle 150 149 72 ||-'''skulstrip erro'''r - part of the cerebellum is missing<<BR>>-wm mistaken as gm creating a pial surf where it shouldn't be (155 134 134)<<BR>>-pial surf cutting into wm surf (78 136 68 & 117 79 117)<<BR>>-dura mistaken as wm (110 132 164) ||-wm lesion at coords 109 98 162 <<BR>>-lateral ventricles not filled in or WM  lesion at coords 100 150 69 ? <<BR>>-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) <<BR>>-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. <<BR>>-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). <<BR>>-aseg - accurately  labeled the section of temporal lobe that is left out of the surface. <<BR>> -aseg - some very posterior occipital lobe is left unlabeled (coords 103  180 52) <<BR>>-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)<<BR>>-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 <<BR>>-topological defect at coords 139 141 165 ? <<BR>>-Pial surface cutting into cerebellum 114 149 57 <<BR>>-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) <<BR>>-aseg - ventricles not labeled all the way  posteriorly. <<BR>>-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 <<BR>>-pial surface not extending all the way in left inferior  lateral ventricle at 161 140 97 <<BR>>-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 <<BR>>-aseg - ok ||N/A ||
||032 ||-WM lesions at coords 137 67 149, 134 62 137, 88 75 124<<BR>>-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<<BR>>-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)<<BR>>-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) <<BR>>-aseg - ventricle labeled wrong coord 105  127 75 ||N/A ||
||039 ||-WM lesions at coordinates 133 93 107, 113 95 105<<BR>>-Surfs off at the posterior portion of left and right lateral ventricle ||-topological defect 132 153 146, 124 151 156, 132 161 56<<BR>>-calcarine labeled as ventricle 151 158 74 ||-surfs are weird around the ventricles (slice ~78)<<BR>>-wm not included in the surfs (coords 122 147 145 & 133 160 65)<<BR>>-dura taken as wm (114 155 153)<<BR>>-pial surf cutting into wm surf (134 151 145) ||-Topological defects at 131 161 57, 124 151 154 <<BR>>-Not sure if this area is calcarine or lateral ventricle at 151 159 72 ||-bad talairach alignment ||-surfs - cutting planes are off. <<BR>>-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<<BR>>-surfs going into inf lat vent ~104 ||-dura taken as wm (95 139 147) <<BR>>-wm or dura?? (140 137 168) ||N/A ||-LH pial surf a bit tangled (slice 92 - vol index 145 142 92) ||-surfs - ok <<BR>>-aseg - ok ||N/A ||
||045 ||-white surface excluding some WM in left temporal lobe<<BR>>-Surfs off near posterior portion of left and right lateral ventricle ||-intensity problem on lh temp lobe ~151<<BR>>-calcarine labeled as ventricle 154 138 64<<BR>>-surfs overlap at ventricle 106 138 73 ||-surfs are messed up around the ventricles (~60)<<BR>>-surfs not including wm (96 149 112 & 84 153 99) ||-topological defect at 160 150 140 ? <<BR>>-Not sure if this area is calcarine  or lateral ventricle 153 139 62 <<BR>>-topological defect at 96 148 112 ||-superior CC cut plane too much in LH <<BR>>-RH pial sur misses a lot of temp  lobe (slice 139) <<BR>>-LH pial sur misses a lot of frontal & temp lobe  (slice 146) ||-surfs - cutting planes off <<BR>>-aseg - ok ||-surfs - temporal lobes better, but still not great. 89 129 141 <<BR>>-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)<<BR>>-pial surf cutting into wm surf (104 153 142)<<BR>> wm surf loop (187 93 98 & 84 104 118) ||N/A ||-not bad overall ||-surfs - ok <<BR>>-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<<BR>>-extra skull left in posterior - cortex overlabeled ||-lat. ventricles surfs are messed up (~44 & ~65)<<BR>>-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. <<BR>>-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) <<BR>>-surfs - pial surfaces include some  non-grey matter in slices 158 and up. <<BR>>-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<<BR>>-Surfs off at posterior portion of left and right lateral ventricles ||-topological defects 128 119 161 & on temporal lobes (low intensity) ~150<<BR>>-intensity problem (147>110) 141 131 41<<BR>>-calcarine labeled as ventricle 155 133 7<<BR>>-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) <<BR>>-surfs - portion of temp lobe excluded  coords 79 119 138<<BR>> -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. <<BR>>-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)<<BR>>-pial surf cutting into wm surf (152 147 88 & 75 104 104)<<BR>>-dura taken as wm (117 134 167) ||-pial surfaces crossing over WM surface at coords 94 81 149, 132 123 146  <<BR>>-WM surface excluding WM -pial surface tangled in all the views (Cor,  Sag, Hor) at 139 137 130 <<BR>>-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 <<BR>>-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<<BR>>-Pial surface crossing white near left lateral ventricle ||topological defect (intensity) 141 133 167<<BR>>-cortex over labeled to cerebellum 141 159 45<<BR>>-cerebellum aseg missing 133 166 45 ||-pial surf cutting into wm surf (133 127 177)<<BR>>-lat. vent. area (95 146 109)<<BR>>-gm taken as wm (94 125 170)<<BR>>-ventr. mistaken as calcarine (128 128 71) ||N/A ||-not bad overall ||-surfs - ok <<BR>>-aseg - ok ||N/A ||
||092 ||-few WM lesions. Otherwise looks okay ||-topological defect 134 137 181 ||-'''skullstrip error '''- part of the cerebellum is missing <<BR>>-dura taken as wm (114 141 166, 170 119 135, 112 139 165 & 174 130 140) ||N/A ||-good overall ||-surfs - ok <<BR>>-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)<<BR>>-loop of wm surf (124 102 181) ||-pial surface curves sharply inwards and also crosses WM surface at  coords 133 123 135 <<BR>>-pial and main surface curve inward again at coords  133 111 117 ||-good overall ||-surfs - ok <<BR>>-aseg - ok ||N/A ||
||095 ||-surfs off around coordinates 88 110 138, 171 107 138<<BR>>-WM lesions in quite a few areas<<BR>>-Surfs slightly off near posterior lateral ventricle of both hemis ||-surfs going in through wm 161 111 128, 87 114 129 <<BR>>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<<BR>>-surfs around calcarine area are messed up (111 162 62)<<BR>>-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 <<BR>>-pial  surface curves sharply inwards at coords 158 123 138, 131 132 131 <<BR>>-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 <<BR>>-surfs - cutting planes HORRIBLE.  bad talairach. <<BR>>-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<<BR>>-extra dura posterior making cortex overlabeled ||-dura taken as wm (117 147 153)<<BR>>-pial surf cutting into wm surf (79 139 140) ||-topological defect at coords 88 144 153. WM mislabelled as grey matter  in aseg <<BR>>-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) <<BR>>-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<<BR>>-wm labeled as gm making surfs messed up near ventricle 93 141 69 ||-lat. vent. area surfs<<BR>>-pial surf cutting into wm surf (94 94 145) ||-topological defect at coords 132 158 57 <<BR>>-Pial surface cutting into Cerebellum at coords 114 161 60 ||-RH frontal lobe surfs on slice 150?  (132 165 150) otherwise good ||-surfs - ok <<BR>>-aseg - ok ||N/A ||
||102 ||-surfs need to be corrected around coordinates 110 59 127 || ||-lat. vent. area<<BR>>-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  <<BR>>-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)<<BR>>-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 <<BR>>-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<<BR>>-extra dura in posterior making cortex overlabeled ||-ventricle mistaken as calcarine (102 118 76)<<BR>>-gm included as wm (123 142 159)<<BR>>-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 <<BR>>-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<<BR>>-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)<<BR>>-ventricle?? (152 124 65) ||-pial surface tangled at coords 83 136 149, 160 154 160 in all the views  <<BR>>-pial surface is excluding some brain tissue. Not sure if it's a  lesion. coords are 105 127 65. Needs WM edits? <<BR>>-in aseg, dura is  labelled as grey matter at coords 124 78 56 ||-very bad -- RH cereb missing, RH temp lobes losing surfs (145) <<BR>> -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 <<BR>>-aseg -129 120 166 non-brain crud  labelled as WM<<BR>> -* * 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<<BR>>-dura taken as wm (115 139 166)<<BR>>-lh lateral ventricle area (~55) ||-pial surface crossing over WM surface at coords 80 86 128 <<BR>>-pial surface curves inward sharply at coords 132 128 145 ||-temporal lobe: disconnection of thin gyri, slices 133-135 <<BR>>-frontal  lobe: misclassification of non-wm as wm, slice 179+-10 <<BR>>-lateral  ventricle: not filled, slice 50-168 ||-surfs - some skull picked up as pial coronal slice 50, LH temp lobe  sucks 166 142 160 <<BR>>-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 <<BR>> -* * 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<<BR>>-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<<BR>>-surfs around ventricle messed up 146 147 57 ||-'''skullstrip error '''- a little bit of cerebellum is stripped off toward posterior <<BR>>-really bad case overall<<BR>>-mesh of pial surf (119 65 101 &17 150 82)<<BR>>dura taken as wm (93 162 69 & 117 120 155)<<BR>>-lh lateral ventricle not filled in all the way (~65)<<BR>>-pial surf cutting into white surf (92 148 86 & 120 118 143) <<BR>> -rh ventricle not filled in (~68) ||-topological defect at 101 74 136 <<BR>>-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)  <<BR>>-surfs - large portion of corpus callosum left out (125 116 88)  normalization problem <<BR>>-aseg - labeling as none around the ventricles  (145 94 144) and here (108 122 95) <<BR>>-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)<<BR>>-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 <<BR>>-aseg - too many NONE voxels  around lateral vents e.g. cor slice 88 ||N/A ||
||124 ||-WM lesions in few areas<<BR>>-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 <<BR>>-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 <<BR>>-aseg - seems ok ||N/A ||
||128 ||-Pial surface cutting in sharply at coords 100 143 79, 157 147 73 ||-topological defect 125 128 148<<BR>>-calcarine labeled as ventricle 148 150 66 ||-pial surf cutting into white surf (96 86 148 & 95 141 146)<<BR>>wm not included in surf (141 156 53) ||N/A ||-not bad overall ||-surfs - ok <<BR>>-aseg - labeling as none around ventricles (109 105 143)  <<BR>>-aseg - poorly labeled wm (labeled as cortex) see SAG slice 118 ||N/A ||
||129 ||-pial surface cutting in sharply at coords 111 112 73<<BR>>-surfs off at posterior portion of left lateral ventricle ||-topological defect 142 109 175<<BR>>-surfs messed up at ventricle 160 104 80<<BR>>-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  <<BR>>-aseg - ok, a lot of post-occipital skull labeled as cortex,  vessel/ganglia causing surf probs 159 105 136 <<BR>>-* * * * 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) <<BR>>-ventricle mistaken as calcarine (99 119 79) ||N/A ||-good overall ||-surfs - pretty good, but some pial tangling in LH 183 133 78 <<BR>>-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<<BR>>-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. <<BR>>-aseg - labeling as none  around ventricles. <<BR>>-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 <<BR>>-aseg - labeling as none around ventricles <<BR>>-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 <<BR>>-lateral ventricles area (~71) ||N/A ||-good overall ||-surfs - ok <<BR>>-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<<BR>>-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 <<BR>>-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)<<BR>>-pial surf cutting into white surf (109 102 200) ||N/A ||-good overall ||-surfs - ok <<BR>>-aseg - lots of voxels labeled none 104 102 102 and 152 100 102 ||N/A ||
||141 ||-WM lesions in few areas<<BR>>-Surfs slightly off at posterior portion of right and left lateral ventricle ||-topological defect 135 112 149<<BR>>-ventricle mistaken as sulcus 107 86 75 ||-lateral ventricles area (~76) <<BR>>-dura taken as wm (172 97 143) ||N/A ||-good overall ||-surfs - ok <<BR>>-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<<BR>>-calcarine labeled as ventricle 147 141 83 ||-'''skullstrip error''' - a bit of lh cerebellum missing<<BR>>-lateral ventricles area (~78)<<BR>>-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, <<BR>>-artifacts in scan (e.g. slice 125) ||-surfs -cutting planes are awful - talairach bad <<BR>>-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<<BR>>-Surfs off at posterior portion of right and left lateral ventricles ||-topological defect tip of both temp lobes ~150<<BR>>-calcarine labeled as ventricle ~70 ||-'''skullstrip error''' - part of the lh temporal lobe is stripped off - fixed by adjusting watershed threshold<<BR>>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 <<BR>>-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)<<BR>>-pial surf cutting into white surf (76 124 95, 117 130 178 & 97 114 178)<<BR>>-dura taken as wm (113 144 164) ||N/A ||-not bad overall ||-surfs - ok <<BR>>-aseg - labeling bad through occip. lobe SAG slice 146 ||N/A ||


*Path of data is: <<BR>>v5.0: /autofs/cluster/freesurfer/test/subjects/x86_64/buckner_data/group_study_fs5.0.0_from_scratch<<BR>>v5.1: /autofs/cluster/freesurfer/test/subjects/x86_64/buckner_data/group_study_fs5.1.0

For more detailed notes of which errors could be fixed and which couldn't, refer to <<BR>>/autofs/cluster/freesurfer/test/subjects/x86_64/buckner_data/group_study_fs5.0.0_from_scratch/notes.ods <<BR>><<BR>>

**40 subjects in the Buckner data set have each been inspected for defects  and following is a brief description of them. recons were launched with  the stable v4.3.0 of Freesurfer.  The data is in the path /autofs/space/birn_045/users/BWH/buckner_data/group_study Couple  of scans from this data set are used as examples to update the  tutorials. Subject 004 is used for Pial edits. Subject 008 is used for  WM lesions and WM and dura labeled as WM. Subject 099 is used as an  example for topological defects. <<BR>><<BR>>

***The 40 subjects in the [[Buckner40Notes/../../fswiki/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).

== Stable 5.0.0 Errors Categorization ==
||<tablewidth="200px"style="text-align: center;" |2>'''Subjid''' ||||||||||||<style="text-align: center;">'''Failure Modes''' ||
||<style="text-align: center;">Segmentation Errors ||<style="text-align: center;">Intensity Normalization ||<style="text-align: center;">Pial Surface Misplacement ||<style="text-align: center;">Skullstrip Errors ||<style="text-align: center;">Topological Errors ||
||004 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||008 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||017 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||021 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||032 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||039 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||040 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||045 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||049 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||067 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||073 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||074 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||080 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||084 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||091 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||092 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||093 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||095 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||097 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||099 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||102 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||103 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||106 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||108 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||111 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||
||114 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||123 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||124 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||128 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||129 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||130 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||131 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||133 ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||136 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||
||138 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||140 ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||141 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;"> ||
||144 ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;">x ||
||145 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;">x ||<style="text-align: center;"> ||
||149 ||<style="text-align: center;"> ||<style="text-align: center;"> ||<style="text-align: center;">x ||<style="text-align: center;"> ||<style="text-align: center;">x ||
||'''Total''' ||<style="font-weight: bold; text-align: center;">13 ||<style="font-weight: bold; text-align: center;">19 ||<style="font-weight: bold; text-align: center;">34 ||<style="font-weight: bold; text-align: center;">9 ||<style="font-weight: bold; text-align: center;">21 ||