<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Alex, thank you for the response. I’ve sent another email with files. <div class=""><br class=""></div><div class="">Denis, yes, I just checked the empty room recordings for the other subjects in this study as well as a recording I obtained some months ago. I am able to open them in Brainstorm but get the same error across all files in MNE-python. I thought I had previously pulled the older empty room recording into a prior version of MNE-Python, but I can’t remember with certainty. </div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Josh</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;">Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy<br class="">13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285 <br class=""> <br class=""></div><br class=""></div>
<div><br class=""><blockquote type="cite" class=""><div class="">On Sep 26, 2018, at 1:25 PM, Denis-Alexander Engemann <<a href="mailto:denis.engemann@gmail.com" class="">denis.engemann@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p><div class=""><br class="webkit-block-placeholder"></div>Keep me in the loop. I may be able to help. Can you btw. exclude that it is an issue for that particular file?<br class=""><div class="gmail_quote"><div dir="ltr" class="">On Wed 26 Sep 2018 at 21:02, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" class="">alexandre.gramfort@inria.fr</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> External Email - Use Caution <br class="">
<br class="">
hi Josh,<br class="">
<br class="">
can you share the empty room data with a script crashes?<br class="">
<br class="">
thanks<br class="">
Alex<br class="">
<br class="">
<br class="">
On Wed, Sep 26, 2018 at 7:57 PM Bear, Joshua <<a href="mailto:JOSHUA.BEAR@ucdenver.edu" target="_blank" class="">JOSHUA.BEAR@ucdenver.edu</a>> wrote:<br class="">
><br class="">
> Hello everyone,<br class="">
><br class="">
> I’m working with some BTI data and would like to include empty room recordings done prior to the patient recordings for my noise covariance. When importing the data using mne.io.read_raw_bti() I have to set convert=False or I get an error. Then, when trying to save the data to the FIF format, I will get the same error, presumably because it is now trying to perform the conversion function that I had previously avoided.<br class="">
><br class="">
> I do not have any problems with the actual subject recordings, only the empty room one.<br class="">
><br class="">
> I’ve included the error message below. Has anyone seen this before and/or have suggestions on how to get my empty room data converted to FIF?<br class="">
><br class="">
> Thank you for your help,<br class="">
> Josh<br class="">
><br class="">
><br class="">
><br class="">
><br class="">
> This is the error that appears to occur during BTI to FIF conversion:<br class="">
><br class="">
> Reading 4D PDF file /mystudy/06%29%18@13:28/1/c,rfhp0.1Hz...<br class="">
> Creating Neuromag info structure ...<br class="">
> ... Setting channel info structure.<br class="">
> ... putting coil transforms in Neuromag coordinates<br class="">
> Traceback (most recent call last):<br class="">
> File "<stdin>", line 1, in <module><br class="">
> File "<string>", line 2, in read_raw_bti<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 729, in verbose<br class="">
> return function(*args, **kwargs)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1398, in read_raw_bti<br class="">
> eog_ch=eog_ch, preload=preload, verbose=verbose)<br class="">
> File "<string>", line 2, in __init__<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 729, in verbose<br class="">
> return function(*args, **kwargs)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1031, in __init__<br class="">
> sort_by_ch_name=sort_by_ch_name, eog_ch=eog_ch)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1209, in _get_bti_info<br class="">
> t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 250, in _convert_coil_trans<br class="">
> t = combine_transforms(invert_transform(dev_ctf_t), bti_dev_t,<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/transforms.py", line 576, in invert_transform<br class="">
> return Transform(trans['to'], trans['from'], linalg.inv(trans['trans']))<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/linalg/basic.py", line 946, in inv<br class="">
> a1 = _asarray_validated(a, check_finite=check_finite)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/_lib/_util.py", line 238, in _asarray_validated<br class="">
> a = toarray(a)<br class="">
> File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/numpy/lib/function_base.py", line 1233, in asarray_chkfinite<br class="">
> "array must not contain infs or NaNs")<br class="">
> ValueError: array must not contain infs or NaNs<br class="">
><br class="">
><br class="">
><br class="">
><br class="">
><br class="">
> Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy<br class="">
> 13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285<br class="">
><br class="">
> External Email - Use Caution<br class="">
><br class="">
> _______________________________________________<br class="">
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