Buckner40 Notes

The 40 subjects in the [wiki:FsTutorial/Data buckner_data/group_study tutorial distribution] have each been inspected for defects. 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


nicks notes: if -clean is used with recon-all, to wipe all edits, then these subjects will run past 72 hours of processing time (and get terminated by seychelles):

subj

notes

093

wm.mgz looks awful

130

080

067

has control.dat edits

040

049

021

039

40 - 50 hrs:

108

004

140

097

136