[Mne_analysis] Error while reading snirf data

[郭垒]

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Dear Eric and Aqil:
Sorry for my late response, I have reported this bug on github Error while reading snirf data · Issue #393 · mne-tools/mne-nirs (github.com) and uploaded the file that can reproduce this bug. Thank you very much for your help.


Lei Guo

At 2021-09-24 11:21:41, "Aqil Izadysadr" <aqil.izadysadr at gmail.com> wrote:

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Dear Eric,

 

I just opened an issue using the GitHub link and shared the Python script giving me the error.

 

Thank you for your assistance!

 

Best,

Aqil

 

From: Eric Larson
Sent: Thursday, September 23, 2021 10:17 AM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Error while reading snirf data

 

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This looks like a bug in the SNIRF writer (or maybe reader?), can you open an issue here and ideally share a file (e.g., on Google Drive, DropBox, etc.) that has this problem:

 

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Eric

 

 

On Wed, Sep 22, 2021 at 7:58 AM 郭垒 <guolei0812 at yeah.net> wrote:

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Dear everyone!

I am trying to use the mne_nirs module to process my fNIRS data. My device is NIRx and it provides snirf output. However, when I use the function mne.io.read_raw_snirf( ), it threw a valueError.  Here below is my error log:

 

data1 = mne.io.read_raw_snirf('./whu0001_001/whu0001_001.snirf',preload=True)

---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

c:\Users\GuoLei\Desktop\test_wtc\data_preprocess.py in 

----> 7 data1 = mne.io.read_raw_snirf('./whu0001_001/whu0001_001.snirf',preload=True)

 

D:\Softwares\Anaconda3\envs\data_analysis\lib\site-packages\mne\io\snirf\_snirf.py in read_raw_snirf(fname, preload, verbose)

     45     mne.io.Raw : Documentation of attribute and methods.

     46     """

---> 47     return RawSNIRF(fname, preload, verbose)

     48 

     49 

 

<decorator-gen-250> in __init__(self, fname, preload, verbose)

 

D:\Softwares\Anaconda3\envs\data_analysis\lib\site-packages\mne\io\snirf\_snirf.py in __init__(self, fname, preload, verbose)

    270                     else:

    271                         extra_ps[f'EEG{len(extra_ps) + 1:03d}'] = diglocs[idx]

--> 272                 info['dig'] = _make_dig_points(nasion=nasion, lpa=lpa, rpa=rpa,

    273                                                hpi=hpi, dig_ch_pos=extra_ps,

    274                                                coord_frame=_frame_to_str[

 

D:\Softwares\Anaconda3\envs\data_analysis\lib\site-packages\mne\io\_digitization.py in _make_dig_points(nasion, lpa, rpa, hpi, extra_points, dig_ch_pos, coord_frame)

    375         lpa = np.asarray(lpa)

    376         if lpa.shape != (3,):

--> 377             raise ValueError('LPA should have the shape (3,) instead of %s'

    378                              % (lpa.shape,))

    379         dig.append({'r': lpa, 'ident': FIFF.FIFFV_POINT_LPA,

 

ValueError: LPA should have the shape (3,) instead of (4,)

---------------------------------------------------------------------------

 

I really have no idea what "LPA" is. I used this function before on another data set (recorded from the same device) and it worked well.  Does anyone have a solution to this error? Thanks advance!

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