[Mne_analysis] mne_edf2fiff error
Song, Daniel
DSONG2 at mgh.harvard.edu
Wed Mar 1 09:46:01 EST 2017
Aha, yes it was the extra line in the hpts file causing the error. Thanks Matti!
Teon -- I have not tried the Python implementation but plan on moving over someday...
Thanks all
Dan Song
Clinical Research Coordinator
Massachusetts General Hospital Neurology Department
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Matti Hamalainen [msh at nmr.mgh.harvard.edu]
Sent: Tuesday, February 28, 2017 8:23 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] mne_edf2fiff error
Hi Dan,
Probably the empty line without a leading # is causing the trouble in mne_edf2fiff
- Matti
On Feb 28, 2017, at 6:11 PM, Teon Brooks <teon.brooks at gmail.com<mailto:teon.brooks at gmail.com>> wrote:
Hi Dan,
The only thing I could see as potentially problematic would be the leading zeros for the cardinal points (and making the hpi as well) in the hpts file. I know that in the Python implementation of MNE, the hpts format is compatible. This implementation is the most up-to-date. I know that the original command line tools should be compatible for hpts but it is not being actively developed anymore. Have you tried using the Python implementation?
HTH,
teon<http://teonbrooks.github.io/>
--
twitter: @teon_io<http://www.twitter.com/teon_io>
On Tue, Feb 28, 2017 at 2:02 PM, Song, Daniel <DSONG2 at mgh.harvard.edu<mailto:DSONG2 at mgh.harvard.edu>> wrote:
Dear MNE users,
I am running into a problem when trying to convert and edf file into a fif file with EEG electrode coordinates. I'm using the command mne_edf2fiff as below:
mne_edf2fiff --edf MGH118_CTvsFspikes.edf --hpts MGH118.hpts --fifout MGH118_CTvsFspikes.fif
This is the output I get:
mne_edf2fiff version 1.9 compiled at Apr 26 2016 04:25:02
EDF/EDF+/BDF file (input) : MGH118_CTvsFspikes.edf
hpts file (input) : MGH118.hpts
fif file (output) : MGH118_CTvsFspikes.fif
Parsing EDF/EDF+/BDF header...[done]
Reading the digitization data from MGH118.hpts (coordinates in millimeters)...
Unknown digitizer point type :
I'm not sure what it means by unknown digitizer point type. I've checked the format of my hpts file and believe it follows the correct format. Contents of my hpts file are below. Anyone have any ideas as to what I'm missing?
Thanks!
#
# This file contains digitization data in the hpts format.
# Cardinal landmark identifiers:
#
# Left auricular = 001
# Nasion = 002
# Right auricular = 003
#
cardinal 0001 -59.95 0 0
cardinal 0002 0 91.6 0
cardinal 0003 83.74 0 0
hpi 0001 -0.46 101.9 21.3
hpi 0002 2.82 98.76 15.96
hpi 0003 0.94 95.24 13.23
hpi 0004 5.87 94.18 23.95
eeg 0000 2.65 95.39 36.05
eeg AF7 -37.97 73.14 33.62
eeg F7 -50.35 54.66 40.98
eeg T1 -58.07 26.11 23.78
eeg AFF5H -37.96 71.27 52.79
eeg F5 -50.35 57.85 46.63
eeg FFT7H -56.62 40.88 44.92
eeg FT7 -64.94 21.17 35.39
eeg FTT9H -61.42 15.27 31.15
eeg F3 -32.48 66.12 65.86
eeg FFC5H -46.99 54.59 58.63
eeg FC5 -59.21 34.36 54.51
eeg FTT7H -62.64 18.41 48.83
eeg T3 -65.73 -0.25 32.56
eeg M1 -58.66 -41.14 -6.6
eeg FFC3H -29.88 56.92 77.83
eeg FC3 -43.76 43.64 72.05
eeg FCC5H -53.68 28.7 70.71
eeg C5 -64.25 2.9 64.59
eeg TTP7H -64.83 -10.83 56.67
eeg TP7 -66.08 -34.52 44.47
eeg TPP9H -56.39 -49.5 30.54
eeg P9 -48.47 -61.04 24.36
eeg FCC3H -43.99 31.75 74.99
eeg C3 -51.16 19.61 74.22
eeg CCP5H -66.49 -9.06 62.36
eeg CP5 -64.71 -24.54 59.74
eeg TPP7H -62.63 -41.31 51.49
eeg T5 -55.15 -48.5 41.28
eeg PPO9H -48.78 -61.25 34.82
eeg PO9 -38.43 -73.6 34.07
eeg CCP3H -38.18 -7.19 101.44
eeg CP3 -46.21 -23.31 93.37
eeg CPP5H -55.48 -38.38 74.97
eeg P5 -52.39 -51.54 63.24
eeg CPP3H -32.22 -27.76 100.45
eeg P3 -38.02 -47.18 87.8
eeg PPO5H -40.49 -58.59 75.37
eeg PO5 -39.5 -70.89 62.22
eeg PO7 -39.65 -71.63 51.18
eeg FP2 34.29 92.34 22
eeg FPZ 6.13 98.7 14.67
eeg FP1 -22.08 91.15 14.69
eeg AFP4H 25.64 93.76 33.25
eeg AFP3H -5.79 95.95 24.42
eeg AF4 41.28 84.42 47.11
eeg AFZ 11.63 93.36 47.68
eeg AF3 -23.21 86.04 46.55
eeg AFF2 32.25 85.59 64.85
eeg AFF1 -0.59 85.29 65.42
eeg F2 43.21 70.55 80.43
eeg FZ 18.24 71.87 90.29
eeg F1 -10.75 59.33 94.14
eeg FFC2H 21.55 67.83 88.7
eeg FFC1H 12.05 67.33 96.39
eeg FC2 41.62 42.56 102.48
eeg FCZ 20.95 58.32 98.8
eeg FC1 0.42 51.7 104.35
eeg FCC2H 42.62 36.53 114.62
eeg FCC1H 17.72 42.91 115.61
eeg C2 54.52 20.76 110.55
eeg CZ 25.96 25.92 116.86
eeg C1 -3.5 26.33 114.14
eeg CCP2H 42.46 9.07 119.59
eeg CCP1H 16.85 10.55 125.16
eeg CP2 49.22 -11.4 116.48
eeg CPZ 26.47 -3.48 121.61
eeg CP1 -0.77 -5.16 121.76
eeg CPP2H 37.18 -24.47 117.69
eeg CPP1H 12.18 -20.87 120.96
eeg P2 43.12 -36.34 108.23
eeg PZ 21.99 -28.15 114
eeg P1 -1.44 -30.06 115.4
eeg PPO2 32.74 -52.95 107.03
eeg PPO1 4.83 -46.84 107.71
eeg PO4 46.16 -57.99 89.04
eeg POZ 12.61 -58.72 92.68
eeg PO3 -20.31 -49.97 89.52
eeg POO4H 26.74 -73.74 76.6
eeg POO3H -4.63 -65.32 80.67
eeg O2 30.09 -75.58 64.35
eeg OZ 11.37 -78.78 70.8
eeg O1 -13.96 -72.55 68.66
eeg POO10H 20.84 -84.17 49.96
eeg OI2H -4.82 -80.9 53.31
eeg OI1H -17.22 -75.93 53.87
eeg POO9H -21.33 -75.19 52.69
eeg EKG/I2 32.11 -78.36 31.28
eeg IZ/CII 4.22 -78.45 39.36
eeg I1 -25.2 -75.61 38.32
eeg AF8 43.95 53.92 87.89
eeg F8 52.49 63.39 73.55
eeg T2 59.31 69.68 62.18
eeg AFF6H 40.94 20.87 104.59
eeg F6 50.68 32.43 94.38
eeg FFT8H 62.29 41.84 76.37
eeg FT8 51.14 47.97 70.51
eeg FTT10H 53.47 72.25 40.1
eeg F4 32.48 -9.98 107.59
eeg FFC6H 50.65 3.46 101.84
eeg FC6 66.27 13.06 92.57
eeg FTT8H 76.24 22.78 77.56
eeg T4 77.11 35.35 63.04
eeg M2 79.96 47.36 46.1
eeg FFC4H 31.83 -35.07 105.78
eeg FC4 42.7 -22.78 103.62
eeg FCC6H 59.31 -9.84 91.93
eeg C6 70.4 -1.11 81.92
eeg TTP8H 80.55 9.7 64.02
eeg TP8 83.08 16.12 53.75
eeg TPP10H 70.62 23.3 32.23
eeg P10 77.1 -40.89 8.48
eeg FCC4H 47 -53.69 97.52
eeg C4 60.96 -43.34 93.15
eeg CCP6H 75.4 -30.64 83.67
eeg CP6 82.22 -20.77 71.26
eeg TPP8H 88.17 -0.93 44.3
eeg T6 86.04 13.86 37.3
eeg PPO10H 84.55 23.35 22.8
eeg PO10 76.12 29.61 -12.63
eeg CCP4H 50.18 -58.79 84.25
eeg CP4 59.18 -52.25 80.79
eeg CPP6H 71.43 -41.73 64.74
eeg P6 79.15 -32.69 51.56
eeg CPP4H 48.35 -72.68 72.11
eeg P4 70.41 -58.23 58.92
eeg PPO6H 76.69 -51.94 40.74
eeg PO6 73.98 -32.38 10.64
eeg PO8 75.13 -20.76 -0.01
Dan Song
Clinical Research Coordinator
Massachusetts General Hospital Neurology Department
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