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Digitization references

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Uzair Hakim
Posts: 1
Topic starter
(@uzhakim)
New Member
Joined: 2 months ago

Hello, 

 

Is it possible to get the reference coordinates for anatomical locations (LPA, RPA, Nz,Iz, Cz)? I understand these can be inferred from the _coordsystem.json file but to remove any inconsistencies across pipelines it would be useful if they're explicitly defined. 

Thanks, 

Uzair

2 Replies
Robert Luke
Posts: 6
(@rob_luke)
Active Member
Joined: 1 year ago

Hi Uzair,

 

The positions you request are in the snirf files under "landmarks". 

 

In python, you can view this landmarks using the code. Note that HP stands for headpoint.

 

In [1]: from snirf import Snirf

In [2]: snirf = Snirf(r'/Users/rluke/Downloads/FRESH-Audio/sub-04/ses-01/nirs/sub-04_ses-01_task-FRESHAUDIO_nirs.snirf')

In [3]: snirf.nirs[0].probe.landmarkLabels
Out[3]:
array(['LPA', 'NASION', 'RPA', 'HP_1', 'HP_2', 'HP_3', 'HP_4', 'HP_5',
'HP_6', 'HP_7', 'HP_8', 'HP_9', 'HP_10', 'HP_11', 'HP_12', 'HP_13',
'HP_14', 'HP_15', 'HP_16', 'HP_17', 'HP_18', 'HP_19', 'HP_20',
'HP_21', 'HP_22', 'HP_23', 'HP_24', 'HP_25', 'HP_26', 'HP_27',
'HP_28', 'HP_29', 'HP_30', 'HP_31', 'HP_32', 'HP_33', 'Fp1', 'Fpz',
'Fp2', 'AF9', 'AF7', 'AF5', 'AF3', 'AF1', 'AFz', 'AF2', 'AF4',
'AF6', 'AF8', 'AF10', 'F9', 'F7', 'F5', 'F3', 'F1', 'Fz', 'F2',
'F4', 'F6', 'F8', 'F10', 'FT9', 'FT7', 'FC5', 'FC3', 'FC1', 'FCz',
'FC2', 'FC4', 'FC6', 'FT8', 'FT10', 'T9', 'T7', 'C5', 'C3', 'C1',
'Cz', 'C2', 'C4', 'C6', 'T8', 'T10', 'TP9', 'TP7', 'CP5', 'CP3',
'CP1', 'CPz', 'CP2', 'CP4', 'CP6', 'TP8', 'TP10', 'P9', 'P7', 'P5',
'P3', 'P1', 'Pz', 'P2', 'P4', 'P6', 'P8', 'P10', 'PO9', 'PO7',
'PO5', 'PO3', 'PO1', 'POz', 'PO2', 'PO4', 'PO6', 'PO8', 'PO10',
'O1', 'Oz', 'O2', 'O9', 'Iz', 'O10', 'T3', 'T5', 'T4', 'T6', 'M1',
'M2', 'A1', 'A2'], dtype='<U6')

In [4]: snirf.nirs[0].probe.landmarkPos3D
Out[4]:
array([[-8.24899918e-02, 3.52726528e-09, -8.98526586e-10],
[ 6.53406019e-12, 1.14046636e-01, -8.95666916e-09],
[ 8.24899970e-02, 3.89309064e-09, 4.76624781e-10],
[-6.11382317e-02, 9.11308462e-02, 3.18348305e-02],
[ 1.43272047e-02, 5.02854686e-02, -3.38980930e-02],
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Meryem Yücel
Posts: 133
Admin
(@mayucel)
Estimable Member
Joined: 2 years ago

@uzhakim, to access the same fields with MATLAB, you can use the following lines while latest Homer3 is on your MATLAB path:

obj = SnirfLoad('filename.snirf');
obj.probe.landmarkLabels
obj.probe.landmarkPos3D
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