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Update spinal levels files generated by the University of Calgary's Phillips Lab based on the Mendez et al. paper #3

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Update spinal levels files generated by the University of Calgary's Phillips Lab based on the Mendez et al. paper #3

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9b7e3c0
add extra spinal levels info L1 - L5
sandrinebedard Feb 13, 2023
b686796
add updated spinal levels
sandrinebedard Feb 13, 2023
ce64bdf
update spinal levels withour reorientation to RPI
sandrinebedard Feb 14, 2023
e854bba
Add unprocessed Phillips Lab PAM50 levels (#5)
joshuacwnewton Feb 14, 2023
d1520ca
Merge branch 'master' into sb/update-spinal-levels
joshuacwnewton Feb 14, 2023
6ad1a93
Remove unprocessed spinal levels
joshuacwnewton Feb 14, 2023
74cac59
Add README.md with updated processing script
joshuacwnewton Feb 14, 2023
b5a1870
add notebook to generate spinal level map
sandrinebedard Apr 3, 2023
bdfdd5f
Attempt to estimate spinal level using intervertebral foramen distance
tzebre Apr 27, 2023
1f588dc
Attempt to estimate spinal level using intervertebral foramen distanc…
tzebre Apr 27, 2023
2e5ee73
data in csv
tzebre Apr 27, 2023
aacbfb3
estimation with dorsal width
tzebre Apr 28, 2023
93a9433
compute the 3D eucledean distance to position rostral and caudal rootlet
sandrinebedard Apr 28, 2023
00b3c6c
add z_ref since z_c is not adeaqute
sandrinebedard Apr 28, 2023
d0b0099
sort by z_c
sandrinebedard Apr 28, 2023
6a2e221
Diameter + width for estimation
tzebre Apr 28, 2023
558672a
Merge remote-tracking branch 'origin/sb/update-spinal-levels' into sb…
tzebre Apr 28, 2023
8f6297f
Revert "Diameter + width for estimation"
tzebre Apr 28, 2023
5fe0d9a
dorsal width and posterior cord
tzebre Apr 28, 2023
80e8884
dorsal width and posterior SC
tzebre Apr 28, 2023
9d8e965
add foramen file and notebbok with STD
tzebre May 1, 2023
d5208ff
clean notebook with and without std 'spinal_level_theo_sandrine_STD'
tzebre May 4, 2023
4b52a2b
remove old notebook
tzebre May 4, 2023
95f796b
add notebook to generate mendez_df.csv with Supp_values
tzebre May 4, 2023
bb07efd
New version of notebook, modif mm to voxel conversion
tzebre May 10, 2023
4bb585f
local commit of graph testing
tzebre May 10, 2023
87d61b5
push commit with graph and ration modification
tzebre May 16, 2023
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Binary file added code/Mendez_lengths.xlsx
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960 changes: 960 additions & 0 deletions code/PAM50_Drez_estimation_from_Mendez2021.ipynb
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811 changes: 811 additions & 0 deletions code/data_process.ipynb
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Binary file added code/label_center_roots_cervical.nii.gz
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169 changes: 169 additions & 0 deletions code/mendez_df.csv
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Original file line number Diff line number Diff line change
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Segment,MEAN,STD,Mesure
C2,11.299999999999999,1.5,DREZ length
C2,12.6,0.8999999999999999,Seg.L at dorsal CE
C2,13.100000000000001,1.0,Seg.L at BE
C2,24.4,0.8,Inf.Art facet to CR distance
C2,15.5,4.2,IF to RR distance
C2,10.600000000000001,0.7000000000000001,IF to CR distance
C2,7.88,0.3,Dorsal width
C3,9.399999999999999,1.9,DREZ length
C3,13.3,0.7000000000000001,Seg.L at dorsal CE
C3,13.200000000000001,0.8999999999999999,Seg.L at BE
C3,25.0,1.7000000000000002,Inf.Art facet to CR distance
C3,16.299999999999997,2.5,IF to RR distance
C3,10.8,2.7,IF to CR distance
C3,7.18,1.11,Dorsal width
C4,11.6,2.2,DREZ length
C4,13.899999999999999,2.0,Seg.L at dorsal CE
C4,14.6,2.5,Seg.L at BE
C4,26.0,1.4000000000000001,Inf.Art facet to CR distance
C4,18.1,2.1,IF to RR distance
C4,10.1,2.0,IF to CR distance
C4,7.11,0.99,Dorsal width
C5,12.4,2.0,DREZ length
C5,15.0,2.2,Seg.L at dorsal CE
C5,14.299999999999999,1.1,Seg.L at BE
C5,23.799999999999997,4.5,Inf.Art facet to CR distance
C5,15.1,2.9,IF to RR distance
C5,9.3,1.9,IF to CR distance
C5,7.11,0.9,Dorsal width
C6,11.5,1.0,DREZ length
C6,13.600000000000001,1.6,Seg.L at dorsal CE
C6,14.7,1.3,Seg.L at BE
C6,24.8,3.9000000000000004,Inf.Art facet to CR distance
C6,17.2,1.2,IF to RR distance
C6,10.3,1.0,IF to CR distance
C6,6.98,0.49,Dorsal width
C7,11.399999999999999,2.3000000000000003,DREZ length
C7,11.7,1.7000000000000002,Seg.L at dorsal CE
C7,14.6,1.5,Seg.L at BE
C7,26.0,2.3000000000000003,Inf.Art facet to CR distance
C7,20.099999999999998,0.8,IF to RR distance
C7,11.799999999999999,0.8999999999999999,IF to CR distance
C7,6.52,0.68,Dorsal width
C8,11.799999999999999,2.8000000000000003,DREZ length
C8,12.5,1.6,Seg.L at dorsal CE
C8,15.5,2.1,Seg.L at BE
C8,19.4,2.7,Inf.Art facet to CR distance
C8,22.7,2.2,IF to RR distance
C8,15.0,2.5,IF to CR distance
C8,5.97,0.91,Dorsal width
T1,12.0,2.2,DREZ length
T1,13.0,2.8000000000000003,Seg.L at dorsal CE
T1,17.3,1.6,Seg.L at BE
T1,22.5,4.4,Inf.Art facet to CR distance
T1,28.1,3.9000000000000004,IF to RR distance
T1,17.0,2.9,IF to CR distance
T1,5.4,1.0,Dorsal width
T2,13.100000000000001,3.1,DREZ length
T2,16.4,5.0,Seg.L at dorsal CE
T2,19.8,4.699999999999999,Seg.L at BE
T2,26.099999999999998,6.2,Inf.Art facet to CR distance
T2,33.4,5.6000000000000005,IF to RR distance
T2,22.0,3.8,IF to CR distance
T2,4.87,0.63,Dorsal width
T3,15.3,2.6,DREZ length
T3,16.1,3.0,Seg.L at dorsal CE
T3,18.1,2.5,Seg.L at BE
T3,30.299999999999997,5.8999999999999995,Inf.Art facet to CR distance
T3,40.5,6.3,IF to RR distance
T3,23.4,5.0,IF to CR distance
T3,4.83,0.64,Dorsal width
T4,18.400000000000002,4.0,DREZ length
T4,22.799999999999997,3.7,Seg.L at dorsal CE
T4,21.8,1.9,Seg.L at BE
T4,28.799999999999997,5.8999999999999995,Inf.Art facet to CR distance
T4,42.0,4.9,IF to RR distance
T4,26.299999999999997,6.3,IF to CR distance
T4,4.7,0.83,Dorsal width
T5,19.6,4.2,DREZ length
T5,22.1,4.9,Seg.L at dorsal CE
T5,20.6,3.4000000000000004,Seg.L at BE
T5,32.400000000000006,6.8999999999999995,Inf.Art facet to CR distance
T5,44.400000000000006,6.1,IF to RR distance
T5,28.1,3.5,IF to CR distance
T5,4.57,0.76,Dorsal width
T6,18.799999999999997,3.9000000000000004,DREZ length
T6,24.8,4.0,Seg.L at dorsal CE
T6,21.6,3.1,Seg.L at BE
T6,31.7,6.4,Inf.Art facet to CR distance
T6,41.6,5.0,IF to RR distance
T6,23.1,5.0,IF to CR distance
T6,4.37,0.54,Dorsal width
T7,20.099999999999998,3.5,DREZ length
T7,24.5,6.0,Seg.L at dorsal CE
T7,23.599999999999998,3.5,Seg.L at BE
T7,33.6,7.7,Inf.Art facet to CR distance
T7,40.099999999999994,7.199999999999999,IF to RR distance
T7,21.200000000000003,5.300000000000001,IF to CR distance
T7,4.64,0.62,Dorsal width
T8,19.0,3.1,DREZ length
T8,25.5,4.5,Seg.L at dorsal CE
T8,24.0,2.5,Seg.L at BE
T8,34.300000000000004,7.800000000000001,Inf.Art facet to CR distance
T8,37.0,8.9,IF to RR distance
T8,22.0,8.100000000000001,IF to CR distance
T8,5.08,0.55,Dorsal width
T9,20.4,3.4000000000000004,DREZ length
T9,23.900000000000002,4.1,Seg.L at dorsal CE
T9,25.099999999999998,2.9,Seg.L at BE
T9,36.4,7.4,Inf.Art facet to CR distance
T9,38.199999999999996,9.9,IF to RR distance
T9,20.2,6.800000000000001,IF to CR distance
T9,5.29,0.4,Dorsal width
T10,19.3,3.7,DREZ length
T10,25.299999999999997,4.4,Seg.L at dorsal CE
T10,26.7,3.5,Seg.L at BE
T10,40.599999999999994,6.800000000000001,Inf.Art facet to CR distance
T10,40.9,9.399999999999999,IF to RR distance
T10,24.0,7.5,IF to CR distance
T10,5.41,0.36,Dorsal width
T11,15.5,3.9000000000000004,DREZ length
T11,22.400000000000002,5.0,Seg.L at dorsal CE
T11,28.5,1.7999999999999998,Seg.L at BE
T11,43.9,6.1,Inf.Art facet to CR distance
T11,46.7,9.1,IF to RR distance
T11,31.0,8.0,IF to CR distance
T11,5.45,0.39,Dorsal width
T12,15.600000000000001,3.5999999999999996,DREZ length
T12,18.400000000000002,2.6,Seg.L at dorsal CE
T12,27.0,2.1,Seg.L at BE
T12,52.0,3.3000000000000003,Inf.Art facet to CR distance
T12,56.8,9.200000000000001,IF to RR distance
T12,38.8,8.0,IF to CR distance
T12,5.89,0.29,Dorsal width
L1,15.2,4.2,DREZ length
L1,17.5,3.5999999999999996,Seg.L at dorsal CE
L1,30.299999999999997,5.8,Seg.L at BE
L1,68.1,5.5,Inf.Art facet to CR distance
L1,68.1,10.3,IF to RR distance
L1,54.699999999999996,11.6,IF to CR distance
L1,5.64,0.5,Dorsal width
L2,11.799999999999999,3.2,DREZ length
L2,14.0,2.6,Seg.L at dorsal CE
L2,29.5,4.1,Seg.L at BE
L2,85.8,5.1,Inf.Art facet to CR distance
L2,82.4,14.0,IF to RR distance
L2,72.2,15.2,IF to CR distance
L2,5.47,0.84,Dorsal width
L3,11.200000000000001,2.5,DREZ length
L3,11.200000000000001,2.6,Seg.L at dorsal CE
L3,31.099999999999998,3.5,Seg.L at BE
L3,105.19999999999999,6.4,Inf.Art facet to CR distance
L3,102.69999999999999,22.3,IF to RR distance
L3,95.1,22.7,IF to CR distance
L3,5.72,0.49,Dorsal width
L4,11.6,1.1,DREZ length
L4,12.5,2.4,Seg.L at dorsal CE
L4,31.099999999999998,5.300000000000001,Seg.L at BE
L4,116.30000000000001,4.699999999999999,Inf.Art facet to CR distance
L4,115.39999999999999,13.100000000000001,IF to RR distance
L4,106.19999999999999,15.600000000000001,IF to CR distance
L4,5.54,0.55,Dorsal width
L5,11.200000000000001,3.1,DREZ length
L5,9.7,3.8,Seg.L at dorsal CE
L5,27.0,4.2,Seg.L at BE
L5,127.10000000000001,4.4,Inf.Art facet to CR distance
L5,126.6,15.0,IF to RR distance
L5,118.69999999999999,17.1,IF to CR distance
L5,4.08,0.11,Dorsal width
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