mne-tools
ENH: import ANT Neuro .CNT files (some code available)
ANT Neuro has a special fileformat (.cnt and .trg files). I could not find any support to import them in MNE. They do have a c-library libeep which you can compile for python. They were so nice to send me a precompiled 64bit linux version (thus I did not really try to compile myself, but should be straight forward) and I did an early sketch of an importer script for MNE-python. You can find this script here. For me this script seems to work nicely. So far without any preload capacities, but using libeep should be straight forward.
As I don't have much experience in mne-python I did not really know any guides to follow. I adapted a mix between the read_eeglab and the read_cnt functions.
If you do use the libeep-tool be sure to include a link to the source somewhere.
Best, Benedikt
Looks really nice.
Would you be able to share some of these files? The CNT reader is a quite recent addition and I remember there being some variation in the file format. It would be an interesting project to try and see if we can make it work without the dependencies to libeep.
I'm not sure if you mean script files or .cnt files. You can use the read_antcnt file if you want. The compiled version of libeep I don't really know and you would have to contact ANT / Robert Smies (the current author of libeep).
If you want a .cnt file & trigger files you can find examples here. These are only bipolar luminance sensor channels, I can try to find a small .cnt EEG file if you need it.
Yeah, I meant the data files, thanks. These should be fine. Maybe I'll have some time next week to see if I can make any sense of it.
Might be worth asking the author of the library for source plus license permission
Hi,
Maintainer of libeep here. Our project is located on sourceforge: https://sourceforge.net/projects/libeep/ We use the LGPL license which means you can include a copy of the code in your project, provided you submit back changes you make and keep a reference to the original code.
That said, go ahead and include our project into MNE. If it's possible in git I would recommend pulling the sources directly from our subversion repo at sourceforge to prevent having old copies when we make updates.
I have not looked in detail in your project yet, so I can't comment on the feasibility of it, but I recommend to not use binaries, but instead compile from source each time a user installs your project. From my own experience I know it can be quite a handful to support binaries on multiple platforms(Windows, Linux, etc).
If you need any information on how to build the sources(simple python-dev suite + cmake should suffice), let me know. You can contact me on my github account or at: rsmies(at)ant-neuro(dot)com
Yours, Robert
thanks Robert
mne-python is meant to be a pure python package to work out of the box on all systems.
to support these files we need to rewrite the readers in pure python
I wonder if file specs for these ANT files are available somewhere. @smeeze @behinger ?
We have a document that describes our riff format. You can find it here: http://eeprobe.ant-neuro.com/doc/cnt_riff.txt
We have made same modifications recently that have not been updated in this document yet. Mainly the adjustment to use 64-bit chunk sizes to allow very large files to be written. Files with these offsets can be recognized with the Riff tag 'RF64' instead of 'RIFF'. This deviates from the riff standard though.
apart from using riff as container format, we also use a variant of huffman coding to compress our sample data. This is described in the document above under the 'data' chunk. There is more to our file format, such as legacy file support, but I doubt you will come across such old files.
Hope this helps.
Has there been any progress on this? I have a .cnt file that fails on load with read_raw_cnt and I am guessing it is because they are from an ANT Neuro system.
no progress AFAIK. We need volunteers to look into it. @jaeilepp is not working with us anymore.
Hi all,
I'm really sorry to open up this issue again after one year, but I'm still struggling with importing ANT Neuro .cnt files with MNE. I started a conversation with @behinger and Robert a long time ago, but I didn't manage to solve the issue. In my specific case, I might need to compile the libeep library on my own since I'm using MacOS, but I was wondering whether the problem has been solved in any other way?
Many thanks.
we don't still yet such a reader. Someone has to take a stab at it.
in the meantime you can convert your files to edf or .set and then use mne?
Since you are on macOS you might want to try the Python bindings of Biosig. I don't know if it supports ANT CNT, but it's worth a try.
Hi,
@agramfort : oh, that's a pity :( I think that @behinger created one, but his solution was specifically designed for ubuntu 64bit if remember correctly. Btw, yes, that's what I'm doing at the moment: using .set to work with MNE. I think I'll also check whether our ANT recording software is able to export the raw files directly into edf or some other mne-supported format.
@cbrnr : thank you, I'll take a look at them and see whether they can help me sort the issue out
Many thanks to both of you!
@agramfort and I looked into possible solutions to this issue.
At the moment, the fix involves compiling the libeep library linked above yourself (or using binaries such as those provided by @behinger) and using the Python bindings by copying files to you site-packages. Unfortunately, this solution is Python 2.7 only. Moving to Python 3 would involve providing our own bindings for this library and this is not a clean solution.
We concluded that a better option and long term solution is to contact ANT and see if they can provide support for their file formats.
ANT recording system(eego) could export edf, .eeg(brainvision) or .cnt(neuroscan).
Hello, are there any advantages to the ANT neuro .cnt format over the neuroscan .cnt format? As mentioned above our ANT system has the ability to export to .cnt(neuroscan) so I'm wondering what would be the motivation to ever export to ANT's format. Is there increased precision?
I emailed someone from ANT Neuro who responded that
It mostly just has a higher bit-depth and more detailed information for events (triggers that have names). With lower bit depth file formats, you may need to apply a high-pass filter first in order to reduce DC offsets.
So it seems the data does not exactly match between ANT Neuro .cnt format and Neuroscan .cnt format
I have no objection to add a reader for ANT data but it just needs to be implemented by someone. Maybe suggest this to ANT engineer? we have received help from different companies in the past to support their file format.
Since our group work extensively with both the ANT-Neuro system and MNE-Python, I just want to chime in here with some updates and tentative paths forward.
Status quo: We still don't have a native reader of ANT-Neuro EEProbe Continuous Data (.cnt) files in MNE-Python. We cannot use the mne.io.read_raw_cnt() method that imports Neuroscan .cnt files for this purpose. They are different file formats that just unfortunately happen to coincide on picking the same .cnt extension.
Tentative solutions:
- Import EEProbe .cnt files in MATLAB with the EEGLAB importer provided by ANT-Neuro here and save as .set files. Then use mne.io.read_raw_eeglab() to read into MNE-Python as a raw object.
- Download the source code of the data I/O library behind the EEGLAB importer (called libeep) here and use the provided python wrapper (import libeep) to read such EEProbe .cnt files. One would then manually create the MNE-Python raw object by grabbing all relevant information from the "cnt" object instance created by libeep. This is done in the functions provided by @behinger by subclassing
mne.io.BaseRaw. - When exporting recordings from the ANT-Neuro laptop, select a different format (BrainVision, EDF+, Neuroscan) from the EEProbe .cnt file format. You can then use appropriate mne.io.read_raw() functions to read them into MNE-Python. This is acceptable except slight differences on bit depth and loss of certain trigger events. For instance the impedance check events are ignored in these different formats, and you don't get the impedance values at the beginning and end of recording. Amplifier disconnect/reconnect events will also be omitted in these other formats (but EEProbe .cnt file do include them)!
I'm personally going with option 1 simply because I do some stuff in MATLAB too. But all are equally viable. Note that the BrainVision files exported by ANT-Neuro all have a missing space between 'Brain' and 'Vision', so you would need to either fix that before reading or adjust the byte length in mne.io.read_raw_brainvision (found by @proloyd).
Next step: The obstacle right now is that most of the source code in libeep is written in C. To conform to MNE-Python's goal of being a standalone Python package, someone needs to completely rewrite these C functions in Python instead of simply adding a Python wrapper. This will likely take a while, and not sure if anyone from ANT-Neuro is going to do it. When I find the time I might just take a stab at this myself, but very unlikely until late 2023.
Next step: The obstacle right now is that most of the source code in libeep is written in C. To conform to MNE-Python's goal of being a standalone Python package, someone needs to completely rewrite these C functions in Python instead of simply adding a Python wrapper. This will likely take a while, and not sure if anyone from ANT-Neuro is going to do it. When I find the time I might just take a stab at this myself, but very unlikely until late 2023.
And as another blocker the license on SourceForge is listed as GPLv2, which is incompatible with MNE-Python's BSD clause. So these functions cannot be used as a reference / looked at while writing equivalent Python code. To be able to do that, you'd have to contact the original authors and get permission to relicense/adapt their code as BSD in MNE-Python.
Download the source code of the data I/O library behind the EEGLAB importer (called libeep) here and use the provided python wrapper (import libeep) to read such EEProbe .cnt files. One would then manually create the MNE-Python raw object by grabbing all relevant information from the "cnt" object instance created by libeep.
One option would be to improve the libeep Python bindings so that it import libeep could have a libeep.read_raw_ant or whatever that returned a libeep.RawANT instance that subclasses mne.io.BaseRaw. The BaseRaw interface has been established for long enough now that I think as long as the _read_segment_file is implemented properly and __init__ creates info properly, it wouldn't be too fragile. The tough part would be creating pip- and conda-installable libraries, but nowadays with cibuildwheel and conda-forge it's not insurmountable.
@larsoner great suggestion... We'd also need the license permission from ANT-Neuro to update their Python bindings of libeep, is that right?
You only need to relicense if you want to include code in MNE-Python. My "One option" / second paragraph above if you license your libeep Python library as GPLv2 as well everything should be okay. No new code is added to MNE-Python so BSD only matters in your pylibeep (or whatever you call it) in that you would subclass BaseRaw (which should be fine -- GPL code can use BSD but not vice-versa).
@mh105 I would consider contacting ANT support to ask them for a Python reader. We managed to get this from EGI/Philips who released mffpy. But it took sometime to get this...
@larsoner I realized what @behinger provided is exactly doing the subclassing mne.io.BaseRaw route. I've updated my comment above so that people know that option 2 above
Download the source code of the data I/O library behind the EEGLAB importer (called libeep) here and use the provided python wrapper (import libeep) to read such EEProbe .cnt files...
is already pretty much set. I agree @agramfort that we should just have a pip installable package from ANT instead of managing the c library ourselves... I'll give it a try to persuade ANT, might cc you guys on the email.
I met the same problem, @agramfort Is there any progress in the contacting ANT support to Python
