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Oct 06, 2022 3:20 pm
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
Oct 25, 2022 5:41 am
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],
Nov 10, 2022 3:28 pm
@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