Deletions are marked like this. | Additions are marked like this. |
Line 9: | Line 9: |
||'''No.'''|| '''Inspection notes''' || | ||'''No.'''|| '''Inspection notes''' (first run 9/19/2005, *second run 9/29/2005: notes marked with *) || |
Line 11: | Line 11: |
|| ||*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)|| |
|
Line 13: | Line 15: |
|| ||*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.|| |
|
Line 14: | Line 21: |
|| ||*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|| |
|
Line 15: | Line 25: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 16: | Line 28: |
|| ||*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|| |
|
Line 17: | Line 31: |
|| ||*surfs - cutting planes are off.|| || ||*aseg - RH/LH boarder is correct here.|| |
|
Line 18: | Line 34: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 21: | Line 39: |
|| ||*surfs - cutting planes off|| || ||*aseg - ok|| |
|
Line 22: | Line 42: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 23: | Line 45: |
|| ||*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)|| |
|
Line 24: | Line 48: |
|| ||*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|| |
|
Line 25: | Line 52: |
|| ||*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.|| |
|
Line 26: | Line 56: |
|| ||*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|| |
|
Line 27: | Line 59: |
|| ||*surfs - portion of temporal lobe excluded coords 101 158 128. control points maybe|| || ||*aseg - portion of missing temporal lobe is accurately labeled in aseg|| |
|
Line 28: | Line 62: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 29: | Line 65: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 30: | Line 68: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 31: | Line 71: |
|| ||*surfs - large portions of RH temporal lobe excludes|| || ||*surfs - cutting planes HORRIBLE. bad talairach. || || ||*aseg - ok|| |
|
Line 32: | Line 75: |
|| ||*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|| |
|
Line 33: | Line 78: |
|| ||*surfs - ok|| || ||*aseg - ok|| |
|
Line 34: | Line 81: |
|| ||*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... || |
|
Line 35: | Line 84: |
|| ||*surfs - cor slice 146 - RH crud included in pial surf 111 132 146|| || ||*aseg - reasonable || |
|
Line 36: | Line 87: |
|| ||*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|| |
|
Line 38: | Line 91: |
|| ||*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|| |
|
Line 41: | Line 97: |
|| ||*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|| |
|
Line 42: | Line 101: |
|| ||*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|| |
|
Line 43: | Line 106: |
|| ||*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|| |
|
Line 44: | Line 109: |
|| ||*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 || |
|
Line 45: | Line 112: |
|| ||*surfs - ok|| || ||*aseg - labeling as none around ventricles (109 105 143)|| || ||*aseg - poorly labeled wm (labeled as cortex) see SAG slice 118|| |
|
Line 46: | Line 116: |
|| ||*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)|| |
|
Line 47: | Line 120: |
|| ||*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|| |
|
Line 48: | Line 123: |
|| ||*surfs - ok - some vessels in pial surface.|| || ||*aseg - labeling as none around ventricles.|| || ||*aseg - skull labeled as cortex see COR slice 157|| |
|
Line 49: | Line 127: |
|| ||*surfs - ok|| || ||*aseg - labeling as none around ventricles|| || ||*aseg - mislabeled wm (111 87 63)|| |
|
Line 50: | Line 131: |
|| ||*surfs - ok|| || ||*aseg - labeling as none around ventricles|| |
|
Line 51: | Line 134: |
|| ||*surfs - some pial tangling and wm of temp. lobe goes and comes back 102 142 126|| || ||*aseg - labeling as none around ventricles|| |
|
Line 52: | Line 137: |
|| ||*surfs - ok|| || ||*aseg - lots of voxels labeled none 104 102 102 and 152 100 102|| |
|
Line 53: | Line 140: |
|| ||*surfs - ok|| || ||*aseg - wm mislabeled as cortex 146 30 111|| |
|
Line 55: | Line 144: |
|| ||*surfs -cutting planes are awful - talairach bad|| || ||*aseg - not great. RH/LH boarder accurate in aseg. || |
|
Line 56: | Line 147: |
|| ||*surfs - ok|| || ||*aseg - eh, ok i guess.|| |
|
Line 57: | Line 150: |
|| ||*surfs - ok|| || ||*aseg - labeling bad through occip. lobe SAG slice 146|| |
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 *) |
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) |
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 |
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 |
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) |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |