IndexError in brainvision.py when calling read_raw_brainvision
- MNE version: e.g. 1.4.2
- operating system: Windows 11 Pro
Hey all,
New to MNE here and having trouble importing files from this chronic pain EEG dataset. Here’s my what I’ve got:
import numpy as np
import mne
import pathlib
import re
p = pathlib.Path(r"<path>\cpCGX_BIDS")
name = (
p / "sub-023" / "eeg" / "sub-023_task-EC_eeg.vhdr"
)
raw = mne.io.read_raw_brainvision(name,eog = [])
This is the output:
Extracting parameters from <path>\cpCGX_BIDS\sub-023\eeg\sub-023_task-EC_eeg.vhdr...
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[2], line 6
2 p = pathlib.Path(r"C:\Users\acate\CTF_Internship\Databases\CGX\cpCGX_BIDS")
3 name = (
4 p / "sub-023" / "eeg" / "sub-023_task-EC_eeg.vhdr"
5 )
----> 6 raw = mne.io.read_raw_brainvision(name,eog = [])
File ~\anaconda3\envs\mne\Lib\site-packages\mne\io\brainvision\brainvision.py:954, in read_raw_brainvision(vhdr_fname, eog, misc, scale, preload, verbose)
914 @fill_doc
915 def read_raw_brainvision(
916 vhdr_fname,
(...)
921 verbose=None,
922 ):
923 """Reader for Brain Vision EEG file.
924
925 Parameters
(...)
952 mne.io.Raw : Documentation of attributes and methods of RawBrainVision.
953 """
--> 954 return RawBrainVision(
955 vhdr_fname=vhdr_fname,
956 eog=eog,
957 misc=misc,
958 scale=scale,
959 preload=preload,
960 verbose=verbose,
961 )
File <decorator-gen-249>:12, in __init__(self, vhdr_fname, eog, misc, scale, preload, verbose)
File ~\anaconda3\envs\mne\Lib\site-packages\mne\io\brainvision\brainvision.py:88, in RawBrainVision.__init__(self, vhdr_fname, eog, misc, scale, preload, verbose)
77 ext = op.splitext(hdr_fname)[-1]
78 ahdr_format = True if ext == ".ahdr" else False
79 (
80 info,
81 data_fname,
82 fmt,
83 order,
84 n_samples,
85 mrk_fname,
86 montage,
87 orig_units,
---> 88 ) = _get_hdr_info(hdr_fname, eog, misc, scale)
90 with open(data_fname, "rb") as f:
91 if isinstance(fmt, dict): # ASCII, this will be slow :(
File ~\anaconda3\envs\mne\Lib\site-packages\mne\io\brainvision\brainvision.py:723, in _get_hdr_info(hdr_fname, eog, misc, scale)
713 # Extract filter units and convert from seconds to Hz if necessary.
714 # this cannot be done as post-processing as the inverse t-f
715 # relationship means that the min/max comparisons don't make sense
(...)
720 # Current practice of clinical electroencephalography.
721 # Lippincott Williams & Wilkins.`, page 40-41
722 header = re.split(r"\s\s+", settings[idx])
--> 723 hp_s = "[s]" in header[hp_col]
724 lp_s = "[s]" in header[lp_col]
726 for i, ch in enumerate(ch_names, 1):
IndexError: list index out of range
I can load the sample MNE data fine, so I suspect it’s something to do with the header file. Each of the .vhdr files in the dataset is in the same format (example below).
Brain Vision Data Exchange Header File Version 1.0
; Data created by the BrainVision Recorder for CGX - V. 2.00.0010
[Common Infos]
Codepage=UTF-8
DataFile=sub-001_task-EC_eeg.eeg
MarkerFile=sub-001_task-EC_eeg.vmrk
DataFormat=BINARY
; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
DataOrientation=MULTIPLEXED
NumberOfChannels=29
; Sampling interval in microseconds
SamplingInterval=2000
[Binary Infos]
BinaryFormat=IEEE_FLOAT_32
[Channel Infos]
; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
; <Resolution in "Unit">,<Unit>, Future extensions..
; Fields are delimited by commas, some fields might be omitted (empty).
; Commas in channel names are coded as "\1".
Ch1=Fp1,,0.0993411,μV
Ch2=Fpz,,0.0993411,μV
Ch3=Fp2,,0.0993411,μV
Ch4=AF7,,0.0993411,μV
Ch5=AF8,,0.0993411,μV
Ch6=F7,,0.0993411,μV
Ch7=F3,,0.0993411,μV
Ch8=Fz,,0.0993411,μV
Ch9=F4,,0.0993411,μV
Ch10=F8,,0.0993411,μV
Ch11=FC5,,0.0993411,μV
Ch12=FC6,,0.0993411,μV
Ch13=T7,,0.0993411,μV
Ch14=C3,,0.0993411,μV
Ch15=Cz,,0.0993411,μV
Ch16=C4,,0.0993411,μV
Ch17=T8,,0.0993411,μV
Ch18=CP5,,0.0993411,μV
Ch19=CP6,,0.0993411,μV
Ch20=P7,,0.0993411,μV
Ch21=P3,,0.0993411,μV
Ch22=Pz,,0.0993411,μV
Ch23=P4,,0.0993411,μV
Ch24=P8,,0.0993411,μV
Ch25=PO7,,0.0993411,μV
Ch26=PO8,,0.0993411,μV
Ch27=O1,,0.0993411,μV
Ch28=Oz,,0.0993411,μV
Ch29=O2,,0.0993411,μV
[Comment]
BrainVision Recorder for CGX - V. 2.00.0010
Amplifier: Quick-32r
A m p l i f i e r S e t u p
============================
Number of channels: 29
Sampling rate [Hz]: 500
Sampling interval [µs]: 2000
Channels
--------
# Name Phys. chn. Resolution / unit
1 Fp1 8 0.0993411 μV
2 Fpz 3 0.0993411 μV
3 Fp2 26 0.0993411 μV
4 AF7 2 0.0993411 μV
5 AF8 30 0.0993411 μV
6 F7 4 0.0993411 μV
7 F3 27 0.0993411 μV
8 Fz 5 0.0993411 μV
9 F4 9 0.0993411 μV
10 F8 28 0.0993411 μV
11 FC5 29 0.0993411 μV
12 FC6 7 0.0993411 μV
13 T7 6 0.0993411 μV
14 C3 25 0.0993411 μV
15 Cz 13 0.0993411 μV
16 C4 10 0.0993411 μV
17 T8 24 0.0993411 μV
18 CP5 15 0.0993411 μV
19 CP6 12 0.0993411 μV
20 P7 20 0.0993411 μV
21 P3 18 0.0993411 μV
22 Pz 22 0.0993411 μV
23 P4 19 0.0993411 μV
24 P8 21 0.0993411 μV
25 PO7 23 0.0993411 μV
26 PO8 14 0.0993411 μV
27 O1 17 0.0993411 μV
28 Oz 11 0.0993411 μV
29 O2 16 0.0993411 μV
==== Recording filters ==========
Disabled
Impedance [kOhm] at: 14:51:16
Fp1: 37.6353
Fpz: 36.8125
Fp2: 43.8188
AF7: 60.421
AF8: 42.1031
F7: 218.427
F3: 625.906
Fz: 384.095
F4: 99.326
F8: 175.817
FC5: 231.566
FC6: 298.465
T7: 297.604
C3: 334.587
Cz: 735.187
C4: 585.155
T8: 147.043
CP5: 413.109
CP6: 179.641
P7: 488.222
P3: 496.329
Pz: 818.33
P4: 1048.96
P8: 125.094
PO7: 394.931
PO8: 255.505
O1: 141.014
Oz: 336.76
O2: 273.144
Is there anything suspicious about this dataset that’s throwing off brainvision.py? Or could the problem lie somewhere else? Appreciate any advice!
