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fNIRS example dataset (BEP030) #305

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Sep 1, 2022
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fNIRS example dataset (BEP030) #305

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023ffdd
Add fNIRS example dataset
rob-luke Jan 27, 2022
74f52c5
Merge branch 'bids-standard:master' into fnirstapping
rob-luke Jun 12, 2022
4341015
Use nirs branch for validator
rob-luke Jun 12, 2022
a4eeed7
Update fnirs_tapping/dataset_description.json
rob-luke Jun 20, 2022
dfe72d0
Merge branch 'bids-standard:master' into fnirstapping
rob-luke Jun 20, 2022
640c296
Fix spacing in name
rob-luke Jun 20, 2022
3935b49
revert link change validator
sappelhoff Sep 1, 2022
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9 changes: 9 additions & 0 deletions README.md
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Expand Up @@ -118,6 +118,7 @@ bids-examples (in alphabetical order).
- [qMRI datasets](#qmri-datasets)
- [PET datasets](#PET-datasets)
- [Microscopy datasets](#microscopy-datasets)
- [fNIRS datasets](#fnirs-datasets)
- [Multimodal datasets](#multimodal-datasets)

### EEG datasets
Expand Down Expand Up @@ -214,6 +215,14 @@ bids-examples (in alphabetical order).
| micr_SEM | @jcohenadad | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions |
| micr_SPIM | @jcohenadad | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each |


### fNIRS datasets

| name | maintained by | description | link to full data |
| ------------- | ------------- | -------------------------------------------------------------------| --------------------------------------- |
| fnirs_tapping | @rob_luke | Example fNIRS measurement with three conditions from five subjects | https://doi.org/10.5281/zenodo.5529797 |


### Multimodal datasets

| name | maintained by | description | mri | meg | eeg | ieeg | genetics | link to full data |
Expand Down
3 changes: 3 additions & 0 deletions fnirs_tapping/README
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This dataset was provided by Robert Luke. If you use this dataset please use the citation below.

Luke, R., & McAlpine, D. (2021). fNIRS Finger Tapping Data in BIDS Format. https://doi.org/10.5281/zenodo.5529797
8 changes: 8 additions & 0 deletions fnirs_tapping/dataset_description.json
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{
"Name": "fNIRS finger tapping experiment",
"BIDSVersion": "1.8.0",
"DatasetType": "raw",
"Authors": [
"Robert Luke"
]
}
24 changes: 24 additions & 0 deletions fnirs_tapping/participants.json
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{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
6 changes: 6 additions & 0 deletions fnirs_tapping/participants.tsv
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participant_id age sex hand
sub-01 34 M n/a
sub-02 32 F n/a
sub-03 26 F n/a
sub-04 20 F n/a
sub-05 53 M n/a
5 changes: 5 additions & 0 deletions fnirs_tapping/sub-01/nirs/sub-01_coordsystem.json
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{
"NIRSCoordinateSystem": "CapTrak",
"NIRSCoordinateSystemDescription": "The X-axis goes from the left preauricular point (LPA) through the right preauricular point (RPA). The Y-axis goes orthogonally to the X-axis through the nasion (NAS). The Z-axis goes orthogonally to the XY-plane through the vertex of the head. This corresponds to a \"RAS\" orientation with the origin of the coordinate system approximately between the ears. See Appendix VIII in the BIDS specification.",
"NIRSCoordinateUnits": "m"
}
25 changes: 25 additions & 0 deletions fnirs_tapping/sub-01/nirs/sub-01_optodes.tsv
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name type x y z template_x template_y template_z
S1 source n/a n/a n/a -0.041613205 0.026799775 0.129904394
S2 source n/a n/a n/a -0.064766865 0.05814257 0.090842577
S3 source n/a n/a n/a -0.071205546 -0.012874273 0.107878609
S4 source n/a n/a n/a -0.085904365 0.018971698 0.065097624
S5 source n/a n/a n/a 0.036941716 0.027483805 0.130221297
S6 source n/a n/a n/a 0.060651337 0.058824146 0.09117718
S7 source n/a n/a n/a 0.067127714 -0.012199232 0.108572549
S8 source n/a n/a n/a 0.081886856 0.020427932 0.065713251
D1 detector n/a n/a n/a -0.037619589 0.063228516 0.115728028
D2 detector n/a n/a n/a -0.041344451 -0.011779611 0.134950029
D3 detector n/a n/a n/a -0.072424247 0.023472932 0.10322219
D4 detector n/a n/a n/a -0.079125927 0.051409291 0.057370046
D5 detector n/a n/a n/a 0.033527173 0.063599683 0.115838813
D6 detector n/a n/a n/a 0.036866395 -0.011397165 0.135367241
D7 detector n/a n/a n/a 0.067915927 0.024682545 0.103666052
D8 detector n/a n/a n/a 0.075310088 0.052268845 0.057876984
D9 detector n/a n/a n/a -0.037738954 0.034082658 0.129491979
D10 detector n/a n/a n/a -0.061454308 0.064438002 0.090610042
D11 detector n/a n/a n/a -0.07282879 -0.005278705 0.107430548
D12 detector n/a n/a n/a -0.084396106 0.027061234 0.065595107
D13 detector n/a n/a n/a 0.040013338 0.020439746 0.130637675
D14 detector n/a n/a n/a 0.064280202 0.051621257 0.091336329
D15 detector n/a n/a n/a 0.065213931 -0.019260368 0.108809282
D16 detector n/a n/a n/a 0.08272091 0.012990608 0.066584023
57 changes: 57 additions & 0 deletions fnirs_tapping/sub-01/nirs/sub-01_task-tapping_channels.tsv
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name type source detector wavelength_nominal units low_cutoff high_cutoff description sampling_frequency status status_description
S1_D1 760 NIRSCWAMPLITUDE S1 D1 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
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S1_D1 850 NIRSCWAMPLITUDE S1 D1 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D2 760 NIRSCWAMPLITUDE S1 D2 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D2 850 NIRSCWAMPLITUDE S1 D2 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D3 760 NIRSCWAMPLITUDE S1 D3 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D3 850 NIRSCWAMPLITUDE S1 D3 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D9 760 NIRSCWAMPLITUDE S1 D9 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S1_D9 850 NIRSCWAMPLITUDE S1 D9 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D1 760 NIRSCWAMPLITUDE S2 D1 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D1 850 NIRSCWAMPLITUDE S2 D1 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D3 760 NIRSCWAMPLITUDE S2 D3 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D3 850 NIRSCWAMPLITUDE S2 D3 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D4 760 NIRSCWAMPLITUDE S2 D4 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D4 850 NIRSCWAMPLITUDE S2 D4 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D10 760 NIRSCWAMPLITUDE S2 D10 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S2_D10 850 NIRSCWAMPLITUDE S2 D10 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D2 760 NIRSCWAMPLITUDE S3 D2 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D2 850 NIRSCWAMPLITUDE S3 D2 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D3 760 NIRSCWAMPLITUDE S3 D3 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D3 850 NIRSCWAMPLITUDE S3 D3 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D11 760 NIRSCWAMPLITUDE S3 D11 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S3_D11 850 NIRSCWAMPLITUDE S3 D11 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D3 760 NIRSCWAMPLITUDE S4 D3 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D3 850 NIRSCWAMPLITUDE S4 D3 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D4 760 NIRSCWAMPLITUDE S4 D4 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D4 850 NIRSCWAMPLITUDE S4 D4 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D12 760 NIRSCWAMPLITUDE S4 D12 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S4_D12 850 NIRSCWAMPLITUDE S4 D12 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D5 760 NIRSCWAMPLITUDE S5 D5 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D5 850 NIRSCWAMPLITUDE S5 D5 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D6 760 NIRSCWAMPLITUDE S5 D6 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D6 850 NIRSCWAMPLITUDE S5 D6 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D7 760 NIRSCWAMPLITUDE S5 D7 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D7 850 NIRSCWAMPLITUDE S5 D7 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D13 760 NIRSCWAMPLITUDE S5 D13 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S5_D13 850 NIRSCWAMPLITUDE S5 D13 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D5 760 NIRSCWAMPLITUDE S6 D5 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D5 850 NIRSCWAMPLITUDE S6 D5 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D7 760 NIRSCWAMPLITUDE S6 D7 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D7 850 NIRSCWAMPLITUDE S6 D7 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D8 760 NIRSCWAMPLITUDE S6 D8 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D8 850 NIRSCWAMPLITUDE S6 D8 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D14 760 NIRSCWAMPLITUDE S6 D14 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S6_D14 850 NIRSCWAMPLITUDE S6 D14 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D6 760 NIRSCWAMPLITUDE S7 D6 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D6 850 NIRSCWAMPLITUDE S7 D6 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D7 760 NIRSCWAMPLITUDE S7 D7 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D7 850 NIRSCWAMPLITUDE S7 D7 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D15 760 NIRSCWAMPLITUDE S7 D15 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S7_D15 850 NIRSCWAMPLITUDE S7 D15 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D7 760 NIRSCWAMPLITUDE S8 D7 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D7 850 NIRSCWAMPLITUDE S8 D7 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D8 760 NIRSCWAMPLITUDE S8 D8 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D8 850 NIRSCWAMPLITUDE S8 D8 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D16 760 NIRSCWAMPLITUDE S8 D16 760.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
S8_D16 850 NIRSCWAMPLITUDE S8 D16 850.0 V 0.0 3.90625 Near Infrared Spectroscopy (continuous wave) 7.8125 good n/a
91 changes: 91 additions & 0 deletions fnirs_tapping/sub-01/nirs/sub-01_task-tapping_events.tsv
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onset duration trial_type value sample
61.824 5.0 Control 1 483
87.296 5.0 Control 1 682
117.632 5.0 Tapping/Right 3 919
146.816 5.0 Tapping/Right 3 1147
181.504 5.0 Control 1 1418
212.864 5.0 Tapping/Left 2 1663
240.64 5.0 Tapping/Left 2 1880
275.712 5.0 Control 1 2154
311.424 5.0 Tapping/Right 3 2433
344.832 5.0 Tapping/Right 3 2694
373.376 5.0 Tapping/Left 2 2917
404.736 5.0 Tapping/Left 2 3162
435.712 5.0 Tapping/Left 2 3404
474.496 5.0 Tapping/Right 3 3707
512.256 5.0 Tapping/Left 2 4002
544.64 5.0 Control 1 4255
570.368 5.0 Tapping/Left 2 4456
609.28 5.0 Tapping/Right 3 4760
635.904 5.0 Control 1 4968
661.504 5.0 Tapping/Left 2 5168
690.56 5.0 Tapping/Right 3 5395
720.256 5.0 Tapping/Left 2 5627
758.144 5.0 Control 1 5923
784.384 5.0 Control 1 6128
819.456 5.0 Tapping/Left 2 6402
847.872 5.0 Control 1 6624
874.368 5.0 Tapping/Left 2 6831
900.48 5.0 Control 1 7035
930.944 5.0 Tapping/Right 3 7273
965.76 5.0 Tapping/Left 2 7545
993.792 5.0 Tapping/Right 3 7764
1021.44 5.0 Control 1 7980
1046.784 5.0 Tapping/Right 3 8178
1080.192 5.0 Tapping/Left 2 8439
1106.56 5.0 Tapping/Right 3 8645
1144.448 5.0 Tapping/Right 3 8941
1182.72 5.0 Tapping/Left 2 9240
1220.48 5.0 Control 1 9535
1254.784 5.0 Tapping/Right 3 9803
1281.408 5.0 Tapping/Left 2 10011
1317.504 5.0 Tapping/Left 2 10293
1354.624 5.0 Tapping/Right 3 10583
1383.936 5.0 Control 1 10812
1416.064 5.0 Tapping/Right 3 11063
1456.0 5.0 Tapping/Right 3 11375
1485.824 5.0 Tapping/Left 2 11608
1513.344 5.0 Tapping/Right 3 11823
1539.2 5.0 Tapping/Left 2 12025
1565.44 5.0 Tapping/Right 3 12230
1604.736 5.0 Tapping/Left 2 12537
1638.016 5.0 Control 1 12797
1673.6 5.0 Tapping/Right 3 13075
1704.96 5.0 Control 1 13320
1734.784 5.0 Control 1 13553
1760.896 5.0 Tapping/Left 2 13757
1791.104 5.0 Tapping/Right 3 13993
1819.008 5.0 Tapping/Left 2 14211
1857.536 5.0 Control 1 14512
1896.832 5.0 Tapping/Left 2 14819
1936.256 5.0 Control 1 15127
1967.232 5.0 Tapping/Right 3 15369
2003.328 5.0 Tapping/Right 3 15651
2043.264 5.0 Tapping/Right 3 15963
2070.144 5.0 Tapping/Left 2 16173
2106.24 5.0 Tapping/Right 3 16455
2132.992 5.0 Control 1 16664
2166.784 5.0 Control 1 16928
2198.4 5.0 Tapping/Right 3 17175
2234.112 5.0 Tapping/Right 3 17454
2270.976 5.0 Control 1 17742
2305.536 5.0 Control 1 18012
2334.848 5.0 Tapping/Right 3 18241
2362.24 5.0 Tapping/Right 3 18455
2393.216 5.0 Control 1 18697
2432.64 5.0 Control 1 19005
2466.304 5.0 Control 1 19268
2505.216 5.0 Tapping/Left 2 19572
2542.72 5.0 Tapping/Left 2 19865
2578.432 5.0 Control 1 20144
2606.336 5.0 Tapping/Left 2 20362
2639.36 5.0 Tapping/Left 2 20620
2677.504 5.0 Tapping/Right 3 20918
2707.328 5.0 Control 1 21151
2735.616 5.0 Control 1 21372
2770.944 5.0 Tapping/Left 2 21648
2806.912 5.0 Control 1 21929
2833.408 5.0 Tapping/Left 2 22136
2869.376 5.0 Control 1 22417
2908.032 5.0 Tapping/Right 3 22719
2938.496 5.0 Tapping/Left 2 22957
18 changes: 18 additions & 0 deletions fnirs_tapping/sub-01/nirs/sub-01_task-tapping_nirs.json
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{
"TaskName": "tapping",
"Manufacturer": "SNIRF",
"PowerLineFrequency": 50,
"SamplingFrequency": 7.8125,
"SoftwareFilters": "n/a",
"RecordingDuration": 2974.464,
"RecordingType": "continuous",
"EEGChannelCount": 0,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"NIRSChannelCount": 56,
"NIRSSourceOptodeCount": 8,
"NIRSDetectorOptodeCount": 16,
"TriggerChannelCount": 0
}
Empty file added fnirs_tapping/sub-01/nirs/sub-01_task-tapping_nirs.snirf
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2 changes: 2 additions & 0 deletions fnirs_tapping/sub-01/sub-01_scans.tsv
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filename acq_time
nirs/sub-01_task-tapping_nirs.snirf 2020-01-01T13:16:16.000000Z
5 changes: 5 additions & 0 deletions fnirs_tapping/sub-02/nirs/sub-02_coordsystem.json
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{
"NIRSCoordinateSystem": "CapTrak",
"NIRSCoordinateSystemDescription": "The X-axis goes from the left preauricular point (LPA) through the right preauricular point (RPA). The Y-axis goes orthogonally to the X-axis through the nasion (NAS). The Z-axis goes orthogonally to the XY-plane through the vertex of the head. This corresponds to a \"RAS\" orientation with the origin of the coordinate system approximately between the ears. See Appendix VIII in the BIDS specification.",
"NIRSCoordinateUnits": "m"
}
25 changes: 25 additions & 0 deletions fnirs_tapping/sub-02/nirs/sub-02_optodes.tsv
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name type x y z template_x template_y template_z
S1 source n/a n/a n/a -0.041613205 0.026799775 0.129904394
S2 source n/a n/a n/a -0.064766865 0.05814257 0.090842577
S3 source n/a n/a n/a -0.071205546 -0.012874273 0.107878609
S4 source n/a n/a n/a -0.085904365 0.018971698 0.065097624
S5 source n/a n/a n/a 0.036941716 0.027483805 0.130221297
S6 source n/a n/a n/a 0.060651337 0.058824146 0.09117718
S7 source n/a n/a n/a 0.067127714 -0.012199232 0.108572549
S8 source n/a n/a n/a 0.081886856 0.020427932 0.065713251
D1 detector n/a n/a n/a -0.037619589 0.063228516 0.115728028
D2 detector n/a n/a n/a -0.041344451 -0.011779611 0.134950029
D3 detector n/a n/a n/a -0.072424247 0.023472932 0.10322219
D4 detector n/a n/a n/a -0.079125927 0.051409291 0.057370046
D5 detector n/a n/a n/a 0.033527173 0.063599683 0.115838813
D6 detector n/a n/a n/a 0.036866395 -0.011397165 0.135367241
D7 detector n/a n/a n/a 0.067915927 0.024682545 0.103666052
D8 detector n/a n/a n/a 0.075310088 0.052268845 0.057876984
D9 detector n/a n/a n/a -0.037738954 0.034082658 0.129491979
D10 detector n/a n/a n/a -0.061454308 0.064438002 0.090610042
D11 detector n/a n/a n/a -0.07282879 -0.005278705 0.107430548
D12 detector n/a n/a n/a -0.084396106 0.027061234 0.065595107
D13 detector n/a n/a n/a 0.040013338 0.020439746 0.130637675
D14 detector n/a n/a n/a 0.064280202 0.051621257 0.091336329
D15 detector n/a n/a n/a 0.065213931 -0.019260368 0.108809282
D16 detector n/a n/a n/a 0.08272091 0.012990608 0.066584023
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