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add support for NIRStar 14.2 files #10147

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mlrocca opened this issue Dec 17, 2021 · 10 comments · Fixed by #10277
Closed

add support for NIRStar 14.2 files #10147

mlrocca opened this issue Dec 17, 2021 · 10 comments · Fixed by #10277
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@mlrocca
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mlrocca commented Dec 17, 2021

Describe the new feature or enhancement

Please provide a clear and concise description of what you want to add or
change.

I am trying to import my fNIRS data with
mne.io.read_raw_nirx("/Users/name/Downloads/PROTOCOLLO_TDCS_FILE_GREZZI/SHAM/CONTROLLI/2018-11-27_002/")
but I have this error message

Loading /Users/name/Downloads/PROTOCOLLO_TDCS_FILE_GREZZI/SHAM/CONTROLLI/2018-11-27_002/
:1: RuntimeWarning: Only import of data from NIRScout devices have been thoroughly tested. You are using a "NIRSport 8x8" device.
mne.io.read_raw_nirx("/Users/name/Downloads/PROTOCOLLO_TDCS_FILE_GREZZI/SHAM/CONTROLLI/2018-11-27_002/")
:1: RuntimeWarning: Extraction of measurement date from NIRX file failed. This can be caused by files saved in certain locales. Please report this as a github issue. The date is being set to January 1st, 2000, instead of "mar 27 nov 2018""18:13:22.559"
mne.io.read_raw_nirx("/Users/name/Downloads/PROTOCOLLO_TDCS_FILE_GREZZI/SHAM/CONTROLLI/2018-11-27_002/")
Out[8]: <RawNIRX | 2018-11-27_002, 40 x 1934 (247.4 s), ~54 kB, data not loaded>

We used a continuous wave NIRS system (NIRSport 8X8, Nirx Medical Technologies LLC, Berlin, Germany). The fNIRS data acquisition software was the NIRStar 14.2 (Version 14, Revision 2, Release Build, 2016-04-15 NIRx Medizintechnik GmbH, Berlin, Germany; www.nirx.net).

Describe your proposed implementation

Describe how you think the feature or improvement should be implemented (e.g.,
as a new method on an existing class? as new capability added to an existing
method?) If you're not sure, please delete this section and the next section.

Please, could you help me to implement a function that can import my data?

Describe possible alternatives

If you've suggested an implementation above, list here any alternative
implementations you can think of, and brief comments explaining why the chosen
implementation is better.

Additional comments

Add any other context or screenshots about the feature request here.

@mlrocca mlrocca added the ENH label Dec 17, 2021
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welcome bot commented Dec 17, 2021

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

@drammock drammock added fNIRS and removed ENH labels Dec 17, 2021
@larsoner
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Can you share the problematic file? Or even better, any chance you could record a little 1 sec data file from this system and share that so we could add it to our tests?

@larsoner
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cc @rob-luke

@mlrocca
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mlrocca commented Dec 17, 2021

Sure,

Please find enclosed an example of data that gives me that issue
2020-01-24_SHAM_CTRL_0050.zip

I am looking forward to hearing from you
.

@rob-luke
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Hi @mlrocca,

Thanks for this very clear report. MNE currently only supports reading NIRx data from NIRStar version 15.0 and above. Whereas, you are trying to read data acquired with NIRStar version 14.2. I don't think the file format changed very much, so adding support might not be too much effort. Could you open a PR to add support for older NIRx files?

@rob-luke
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This might also be related to #7891 where we had issues handling dates with formats other than Australian English.

@mlrocca
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mlrocca commented Dec 20, 2021

Thank you,

I opened a new issue to add support for older NIRx versions.

If there is also the issue of the dates, is it possible to fix that too?

Best,

@drammock drammock changed the title issue importing fNIRS data in mne add support for NIRStar 14.2 files Dec 20, 2021
@drammock drammock added the ENH label Dec 20, 2021
@mlrocca
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mlrocca commented Dec 20, 2021

Ok thank you,

how long do you think you will take to implement that feature?

Are you going to advice me when it will be implemented?

@drammock
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Ok thank you,

how long do you think you will take to implement that feature?

I don't know. The winter holidays mean many of our developers are not available right now.

Are you going to advice me when it will be implemented?

The pull request that fixes the issue will be linked here and will automatically close this issue when it is merged in. Unless you've disabled it in your GitHub notification settings, you will get a notification when that happens.

@mlrocca
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mlrocca commented Jan 31, 2022

Hi,

any update on the implementation of the feature in the object?

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4 participants