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Zero padded channel labels don't seem to read correctly in the electrodes.tsv file

See original GitHub issue

Describe the bug

I have a BIDS complaint database that I created to use mne’s data processing pipelines on. The read_raw_bids function executes relatively successfully, but doesn’t seem to keep all of my channel locations intact. Upon investigation, it appears that this is because some of the channel labels have zero padding to keep the names consistent (a practice often used in the BIDS specification), and that channels with said padding end up lost.

Steps to reproduce

Here is the contents of the electrodes.tsv file in question:

name	x	y	z	size	hemisphere
LAMT12	-49.0	4.333	-22.667	0.2	LD
LAMT11	-46.0555	4.333	-22.7225	0.2	LD
LAMT10	-43.111	4.333	-22.778	0.2	LD
LAMT09	-40.1665	4.333	-22.8335	0.2	LD
LAMT08	-37.222	4.333	-22.889	0.2	LD
LAMT07	-34.2775	4.333	-22.9445	0.2	LD
LAMT06	-31.333	4.333	-23.0	0.2	LD
LAMT05	-27.9522	4.3806	-23.1428	0.2	LD
LAMT04	-24.5714	4.4282	-23.2856	0.2	LD
LAMT03	-21.1906	4.4758	-23.4284	0.2	LD
LAMT02	-17.8098	4.5234	-23.5712	0.2	LD
LAMT01	-14.429	4.571	-23.714	0.2	LD
LAST08	-54.0	-2.667	-9.667	0.2	LD
LAST07	-50.333	-2.667	-10.0	0.2	LD
LAST06	-46.667	-2.667	-10.0	0.2	LD
LAST05	-43.4753	-2.7003	-9.975	0.2	LD
LAST04	-40.2835	-2.7335	-9.95	0.2	LD
LAST03	-37.0917	-2.7668	-9.925	0.2	LD
LAST02	-33.9	-2.8	-9.9	0.2	LD
LAST01	-30.55	-2.8222	-9.9388	0.2	LD
LPO10	-37.0	-80.333	16.333	0.2	LD
LPO09	-34.8	-78.4	14.4	0.2	LD
LPO08	-32.72	-76.4	12.48	0.2	LD
LPO07	-30.64	-74.4	10.56	0.2	LD
LPO06	-28.56	-72.4	8.64	0.2	LD
LPO05	-26.48	-70.4	6.72	0.2	LD
LPO04	-24.4	-68.4	4.8	0.2	LD
LPO03	-22.0	-66.2	2.8	0.2	LD
LPO02	-19.8571	-64.181	0.8667	0.2	LD
LPO01	-17.7143	-62.162	-1.0666	0.2	LD
LAO16	-54.2778	-68.7778	14.0	0.2	LD
LAO15	-50.8889	-67.8889	14.5	0.2	LD
LAO14	-47.5	-67.0	15.0	0.2	LD
LAO13	-44.0	-66.5	16.0	0.2	LD
LAO12	-41.0	-65.5	16.0	0.2	LD
LAO11	-37.5714	-64.5714	16.5	0.2	LD
LAO10	-34.1429	-63.6429	17.0	0.2	LD
LAO09	-30.7143	-62.7143	17.5	0.2	LD
LAO08	-27.2857	-61.7857	18.0	0.2	LD
LAO07	-23.8571	-60.8571	18.5	0.2	LD
LAO06	-20.4286	-59.9286	19.0	0.2	LD
LAO05	-17.0	-59.0	19.5	0.2	LD
LAO04	-13.6111	-58.1111	20.0	0.2	LD
LAO03	-10.2222	-57.2222	20.5	0.2	LD
LAO02	-6.8333	-56.3333	21.0	0.2	LD
LAO01	-3.4444	-55.4444	21.5	0.2	LD
LPIT16	-54.5417	-45.625	-4.5833	0.2	LD
LPIT15	-52.0	-45.5	-4.0	0.2	LD
LPIT14	-48.5	-46.0	-3.0	0.2	LD
LPIT13	-46.15	-45.85	-2.5	0.2	LD
LPIT12	-43.8	-45.7	-2.0	0.2	LD
LPIT11	-41.45	-45.55	-1.5	0.2	LD
LPIT10	-39.1	-45.4	-1.0	0.2	LD
LPIT09	-36.75	-45.25	-0.5	0.2	LD
LPIT08	-34.4	-45.1	0.0	0.2	LD
LPIT07	-32.05	-44.95	0.5	0.2	LD
LPIT06	-29.7	-44.8	1.0	0.2	LD
LPIT05	-27.35	-44.65	1.5	0.2	LD
LPIT04	-25.0	-44.5	2.0	0.2	LD
LPIT03	-21.5	-44.0	3.0	0.2	LD
LPIT02	-18.9583	-43.875	3.5833	0.2	LD
LPIT01	-16.4167	-43.75	4.1667	0.2	LD
LPSP16	-58.167	-39.833	43.0	0.2	LD
LPSP15	-54.75	-38.75	42.25	0.2	LD
LPSP14	-51.3819	-37.9652	41.7292	0.2	LD
LPSP13	-48.0138	-37.1805	41.2083	0.2	LD
LPSP12	-44.6457	-36.3957	40.6875	0.2	LD
LPSP11	-41.2777	-35.611	40.1667	0.2	LD
LPSP10	-37.9096	-34.8262	39.6458	0.2	LD
LPSP09	-34.5415	-34.0415	39.125	0.2	LD
LPSP08	-31.1734	-33.2567	38.6042	0.2	LD
LPSP07	-27.8053	-32.472	38.0833	0.2	LD
LPSP06	-24.4372	-31.6872	37.5625	0.2	LD
LPSP05	-21.0692	-30.9025	37.0417	0.2	LD
LPSP04	-17.7011	-30.1177	36.5208	0.2	LD
LPSP03	-14.333	-29.333	36.0	0.2	LD
LPSP02	-10.9611	-28.5253	35.4615	0.2	LD
LPSP01	-7.5893	-27.7176	34.9231	0.2	LD
LPIP16	-53.4	-42.4	31.8	0.2	LD
LPIP15	-49.25	-41.75	31.5	0.2	LD
LPIP14	-45.3583	-40.9083	31.45	0.2	LD
LPIP13	-41.4666	-40.0666	31.4	0.2	LD
LPIP12	-37.5749	-39.2249	31.35	0.2	LD
LPIP11	-33.6832	-38.3832	31.3	0.2	LD
LPIP10	-29.7915	-37.5415	31.25	0.2	LD
LPIP09	-25.8998	-36.6998	31.2	0.2	LD
LPIP08	-22.0081	-35.8581	31.15	0.2	LD
LPIP07	-18.1164	-35.0164	31.1	0.2	LD
LPIP06	-14.2247	-34.1747	31.05	0.2	LD
LPIP05	-10.333	-33.333	31.0	0.2	LD
LPIP04	-7.0	-32.5	31.0	0.2	LD
LPIP03	-3.0	-31.5	31.0	0.2	LD
LPIP02	0.8769	-30.6615	30.9385	0.2	LD
LPIP01	4.7538	-29.8231	30.8769	0.2	LD
LPST10	-59.2428	-27.4276	16.44	0.2	LD
LPST09	-55.769	-26.923	15.0	0.2	LD
LPST08	-52.2267	-26.3423	13.55	0.2	LD
LPST07	-48.6845	-25.7615	12.1	0.2	LD
LPST06	-45.1423	-25.1808	10.65	0.2	LD
LPST05	-41.6	-24.6	9.2	0.2	LD
LPST04	-38.4	-24.4	7.8	0.2	LD
LPST03	-34.9262	-23.8954	6.36	0.2	LD
LPST02	-31.4524	-23.3908	4.92	0.2	LD
LPST01	-27.9786	-22.8862	3.48	0.2	LD
LMMT14	-57.5	-22.5	-2.0	0.2	LD
LMMT13	-54.0	-22.25	-3.0	0.2	LD
LMMT12	-50.5	-21.5	-4.0	0.2	LD
LMMT11	-47.1944	-20.9167	-4.7222	0.2	LD
LMMT10	-43.8889	-20.3333	-5.4444	0.2	LD
LMMT09	-40.5833	-19.75	-6.1667	0.2	LD
LMMT08	-37.2778	-19.1667	-6.8889	0.2	LD
LMMT07	-33.9722	-18.5833	-7.6111	0.2	LD
LMMT06	-30.6667	-18.0	-8.3333	0.2	LD
LMMT05	-27.3611	-17.4167	-9.0556	0.2	LD
LMMT04	-24.0556	-16.8333	-9.7778	0.2	LD
LMMT03	-20.75	-16.25	-10.5	0.2	LD
LMMT02	-17.4091	-15.6818	-11.2727	0.2	LD
LMMT01	-14.0682	-15.1136	-12.0455	0.2	LD
LMIT10	-57.75	-31.75	-6.75	0.2	LD
LMIT09	-54.4	-31.8	-7.6	0.2	LD
LMIT08	-50.97	-31.79	-8.33	0.2	LD
LMIT07	-47.54	-31.78	-9.06	0.2	LD
LMIT06	-44.11	-31.77	-9.79	0.2	LD
LMIT05	-40.68	-31.76	-10.52	0.2	LD
LMIT04	-37.25	-31.75	-11.25	0.2	LD
LMIT03	-33.667	-31.667	-12.0	0.2	LD
LMIT02	-30.2266	-31.6552	-12.75	0.2	LD
LMIT01	-26.7862	-31.6433	-13.5	0.2	LD

Expected results

Expected code to read channel labels correctly, and assign labels to locations in the digital montage.

Actual results

TypeError: not all arguments converted during string formatting
Call stack:
  File "c:\Users\ae166\share\git\IEEG_toolboxes\Python\PreProcess\preProcess.py", line 278, in <module>
    filt_main_2(layout)
  File "c:\Users\ae166\share\git\IEEG_toolboxes\Python\PreProcess\preProcess.py", line 250, in filt_main_2
    raw_data = raw_from_layout(layout, sub_id, run)
  File "c:\Users\ae166\share\git\IEEG_toolboxes\Python\PreProcess\preProcess.py", line 189, in raw_from_layout
    new_raw = read_raw_bids(bids_path=BIDS_path)
  File "<decorator-gen-586>", line 24, in read_raw_bids
  File "C:\Users\ae166\Anaconda3\envs\preprocess\lib\site-packages\mne_bids\read.py", line 722, in read_raw_bids
    _read_dig_bids(electrodes_fname, coordsystem_fname,
  File "C:\Users\ae166\Anaconda3\envs\preprocess\lib\site-packages\mne_bids\dig.py", line 519, in _read_dig_bids
    montage = _handle_electrodes_reading(electrodes_fpath, coord_frame,
  File "C:\Users\ae166\Anaconda3\envs\preprocess\lib\site-packages\mne_bids\dig.py", line 42, in _handle_electrodes_reading
    logger.info("The read in electrodes file is: \n", summary_str)
Message: 'The read in electrodes file is: \n'
Arguments: ([('name', ['LAMT12', 'LAMT11', 'LAMT10', 'LAMT09', 'LAMT08', 'LAMT07', 'LAMT06', 'LAMT05', 'LAMT04', 'LAMT03', 'LAMT02', 'LAMT01', 'LAST08', 'LAST07', 'LAST06', 'LAST05', 'LAST04', 'LAST03', 'LAST02', 'LAST01', 'LPO10', 'LPO09', 'LPO08', 'LPO07', 'LPO06', 'LPO05', 'LPO04', 'LPO03', 'LPO02', 'LPO01', 'LAO16', 'LAO15', 'LAO14', 'LAO13', 'LAO12', 'LAO11', 'LAO10', 'LAO09', 'LAO08', 'LAO07', 'LAO06', 'LAO05', 'LAO04', 'LAO03', 'LAO02', 'LAO01', 'LPIT16', 'LPIT15', 'LPIT14', 'LPIT13', 'LPIT12', 'LPIT11', 'LPIT10', 'LPIT09', 'LPIT08', 'LPIT07', 'LPIT06', 'LPIT05', 'LPIT04', 'LPIT03', 'LPIT02', 'LPIT01', 'LPSP16', 'LPSP15', 'LPSP14', 'LPSP13', 'LPSP12', 'LPSP11', 'LPSP10', 'LPSP09', 'LPSP08', 'LPSP07', 'LPSP06', 'LPSP05', 'LPSP04', 'LPSP03', 'LPSP02', 'LPSP01', 'LPIP16', 'LPIP15', 'LPIP14', 'LPIP13', 'LPIP12', 'LPIP11', 'LPIP10', 'LPIP09', 'LPIP08', 'LPIP07', 'LPIP06', 'LPIP05', 'LPIP04', 'LPIP03', 'LPIP02', 'LPIP01', 'LPST10', 'LPST09', 'LPST08', 'LPST07', 'LPST06', 'LPST05', 'LPST04', 'LPST03', 'LPST02', 'LPST01', 'LMMT14', 'LMMT13', 'LMMT12', 'LMMT11', 'LMMT10', 'LMMT09', 'LMMT08', 'LMMT07', 'LMMT06', 'LMMT05', 'LMMT04', 'LMMT03', 'LMMT02', 'LMMT01', 'LMIT10', 'LMIT09', 'LMIT08', 'LMIT07', 'LMIT06', 'LMIT05', 'LMIT04', 'LMIT03', 'LMIT02', 'LMIT01']), ('x', ['-49.0', '-46.0555', '-43.111', '-40.1665', '-37.222', '-34.2775', '-31.333', '-27.9522', '-24.5714', '-21.1906', '-17.8098', '-14.429', '-54.0', '-50.333', '-46.667', '-43.4753', '-40.2835', '-37.0917', '-33.9', '-30.55', '-37.0', '-34.8', '-32.72', '-30.64', '-28.56', '-26.48', '-24.4', '-22.0', '-19.8571', '-17.7143', '-54.2778', '-50.8889', '-47.5', '-44.0', '-41.0', '-37.5714', '-34.1429', '-30.7143', '-27.2857', '-23.8571', '-20.4286', '-17.0', '-13.6111', '-10.2222', '-6.8333', '-3.4444', '-54.5417', '-52.0', '-48.5', '-46.15', '-43.8', '-41.45', '-39.1', '-36.75', '-34.4', '-32.05', '-29.7', '-27.35', '-25.0', '-21.5', '-18.9583', '-16.4167', '-58.167', '-54.75', '-51.3819', '-48.0138', '-44.6457', '-41.2777', '-37.9096', '-34.5415', '-31.1734', '-27.8053', '-24.4372', '-21.0692', '-17.7011', '-14.333', '-10.9611', '-7.5893', '-53.4', '-49.25', '-45.3583', '-41.4666', '-37.5749', '-33.6832', '-29.7915', '-25.8998', '-22.0081', '-18.1164', '-14.2247', '-10.333', '-7.0', '-3.0', '0.8769', '4.7538', '-59.2428', '-55.769', '-52.2267', '-48.6845', '-45.1423', '-41.6', '-38.4', '-34.9262', '-31.4524', '-27.9786', '-57.5', '-54.0', '-50.5', '-47.1944', '-43.8889', '-40.5833', '-37.2778', '-33.9722', '-30.6667', '-27.3611', '-24.0556', '-20.75', '-17.4091', '-14.0682', '-57.75', '-54.4', '-50.97', '-47.54', '-44.11', '-40.68', '-37.25', '-33.667', '-30.2266', '-26.7862']), ('y', ['4.333', '4.333', '4.333', '4.333', '4.333', '4.333', '4.333', '4.3806', '4.4282', '4.4758', '4.5234', '4.571', '-2.667', '-2.667', '-2.667', '-2.7003', '-2.7335', '-2.7668', '-2.8', '-2.8222', '-80.333', '-78.4', '-76.4', 
'-74.4', '-72.4', '-70.4', '-68.4', '-66.2', '-64.181', '-62.162', '-68.7778', '-67.8889', '-67.0', '-66.5', '-65.5', '-64.5714', '-63.6429', '-62.7143', '-61.7857', '-60.8571', '-59.9286', '-59.0', '-58.1111', '-57.2222', '-56.3333', '-55.4444', '-45.625', '-45.5', '-46.0', '-45.85', '-45.7', '-45.55', '-45.4', '-45.25', '-45.1', '-44.95', '-44.8', '-44.65', '-44.5', '-44.0', '-43.875', '-43.75', '-39.833', '-38.75', '-37.9652', '-37.1805', '-36.3957', '-35.611', '-34.8262', '-34.0415', '-33.2567', '-32.472', '-31.6872', '-30.9025', '-30.1177', '-29.333', '-28.5253', '-27.7176', '-42.4', '-41.75', '-40.9083', '-40.0666', '-39.2249', '-38.3832', '-37.5415', '-36.6998', '-35.8581', '-35.0164', '-34.1747', '-33.333', '-32.5', '-31.5', '-30.6615', '-29.8231', '-27.4276', '-26.923', '-26.3423', '-25.7615', '-25.1808', '-24.6', '-24.4', '-23.8954', '-23.3908', '-22.8862', '-22.5', '-22.25', '-21.5', '-20.9167', '-20.3333', '-19.75', '-19.1667', '-18.5833', '-18.0', '-17.4167', '-16.8333', '-16.25', '-15.6818', '-15.1136', '-31.75', '-31.8', '-31.79', '-31.78', '-31.77', '-31.76', '-31.75', '-31.667', '-31.6552', '-31.6433']), ('z', ['-22.667', '-22.7225', '-22.778', '-22.8335', '-22.889', '-22.9445', '-23.0', '-23.1428', '-23.2856', 
'-23.4284', '-23.5712', '-23.714', '-9.667', '-10.0', '-10.0', '-9.975', '-9.95', '-9.925', '-9.9', '-9.9388', '16.333', '14.4', '12.48', '10.56', '8.64', '6.72', '4.8', '2.8', '0.8667', '-1.0666', '14.0', '14.5', '15.0', '16.0', '16.0', '16.5', '17.0', '17.5', '18.0', '18.5', '19.0', '19.5', '20.0', '20.5', '21.0', '21.5', '-4.5833', '-4.0', '-3.0', '-2.5', '-2.0', '-1.5', '-1.0', '-0.5', '0.0', '0.5', '1.0', '1.5', '2.0', '3.0', '3.5833', '4.1667', '43.0', '42.25', '41.7292', '41.2083', '40.6875', '40.1667', '39.6458', '39.125', '38.6042', '38.0833', '37.5625', '37.0417', '36.5208', '36.0', '35.4615', '34.9231', '31.8', '31.5', '31.45', '31.4', '31.35', '31.3', '31.25', '31.2', '31.15', '31.1', '31.05', '31.0', '31.0', '31.0', '30.9385', '30.8769', '16.44', '15.0', '13.55', '12.1', '10.65', '9.2', '7.8', '6.36', '4.92', '3.48', '-2.0', '-3.0', '-4.0', '-4.7222', '-5.4444', '-6.1667', '-6.8889', '-7.6111', '-8.3333', '-9.0556', '-9.7778', '-10.5', '-11.2727', '-12.0455', '-6.75', '-7.6', '-8.33', '-9.06', '-9.79', '-10.52', '-11.25', '-12.0', '-12.75', '-13.5']), ('size', ['0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2', '0.2'])],)
c:\Users\ae166\share\git\IEEG_toolboxes\Python\PreProcess\preProcess.py:189: RuntimeWarning: Fiducial point nasion not found, assuming identity unknown to head transformation
  new_raw = read_raw_bids(bids_path=BIDS_path)
c:\Users\ae166\share\git\IEEG_toolboxes\Python\PreProcess\preProcess.py:189: RuntimeWarning: DigMontage is only a subset of info. There are 89 channel positions not present in the DigMontage. The required channels are:

['LPSP1', 'LPSP2', 'LPSP3', 'LPSP4', 'LPSP5', 'LPSP6', 'LPSP7', 'LPSP8', 'LPSP9', 'LPIP1', 'LPIP2', 'LPIP3', 'LPIP4', 'LPIP5', 'LPIP6', 'LPIP7', 'LPIP8', 'LPIP9', 'LAST1', 'LAST2', 'LAST3', 'LAST4', 'LAST5', 
'LAST6', 'LAST7', 'LAST8', 'LPST1', 'LPST2', 'LPST3', 'LPST4', 'LPST5', 'LPST6', 'LPST7', 'LPST8', 'LPST9', 'LAMT1', 'LAMT2', 'LAMT3', 'LAMT4', 'LAMT5', 'LAMT6', 'LAMT7', 'LAMT8', 'LAMT9', 'LMMT1', 'LMMT2', 'LMMT3', 'LMMT4', 'LMMT5', 'LMMT6', 'LMMT7', 'LMMT8', 'LMMT9', 'LMIT1', 'LMIT2', 'LMIT3', 'LMIT4', 'LMIT5', 'LMIT6', 'LMIT7', 'LMIT8', 'LMIT9', 'LPIT1', 'LPIT2', 'LPIT3', 'LPIT4', 'LPIT5', 'LPIT6', 'LPIT7', 'LPIT8', 'LPIT9', 'LAO1', 'LAO2', 'LAO3', 'LAO4', 'LAO5', 'LAO6', 'LAO7', 'LAO8', 'LAO9', 'LPO1', 'LPO2', 'LPO3', 'LPO4', 'LPO5', 'LPO6', 'LPO7', 'LPO8', 'LPO9'].

Consider using inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.

Additional information

Platform:       Windows-10-10.0.18362-SP0
Python:         3.9.7 (default, Sep 16 2021, 16:59:28) [MSC v.1916 64 bit (AMD64)]
Executable:     C:\Users\ae166\Anaconda3\envs\preprocess\python.exe
CPU:            Intel64 Family 6 Model 158 Stepping 9, GenuineIntel: 8 cores
Memory:         63.9 GB

mne:            0.24.1
numpy:          1.22.1 {}
scipy:          1.8.0
matplotlib:     3.5.1 {backend=QtAgg}

sklearn:        1.0.2
numba:          Not found
nibabel:        3.2.1
nilearn:        0.8.1
dipy:           1.4.1
cupy:           Not found
pandas:         1.3.5
mayavi:         4.7.4
pyvista:        0.33.2 {OpenGL 4.5.0 - Build 27.20.100.8854 via Intel(R) HD Graphics 630}
pyvistaqt:      0.7.0
ipyvtklink:     0.2.2
vtk:            9.1.0
PyQt5:          5.15.6
ipympl:         0.8.7
mne_qt_browser: Not found
pooch:          v1.4.0

Issue Analytics

State:
Created 2 years ago
Comments:6 (4 by maintainers)

Top GitHub Comments

1reaction

Aaronearlerichardsoncommented, Feb 9, 2022

Ahah! I checked the .edf file header and you’re right the labels were different. False alarm! Thank you for your time.

0reactions

mmagnuskicommented, Feb 9, 2022

@Aaronearlerichardson If the channel labels are different in the electrode positions file than in the data file, they will not be read correctly. You should either change the channel labels in the electrode positions file (removing the zero prefixes) or change the labels in the data file (adding the zero prefixes).

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