Buckner40 Notes
see also: Buckner40Testing
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 |