Extracting Information from -tfr.h5 Files

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1

MNE Version: 0.22.0
OS: Windows 10

I’ve generated -tfr.h5 files for making time frequency graphs. However, I’d like to extract and use the data within the .h5 files to create alternative data comparisons. I found the following on StackOverflow and thought it would be a good starting point for me: hdf5 - Open h5 file to use with MNE python - Stack Overflow

While I begin trying to navigate through the files as per the above example, I wanted to know if I could get some specific feedback here related to the information that I want to extract.

Specifically, I’d like to get the actual values (then the average) of the power of a range of frequencies (for example, 8-12Hz) within specific time points (for example 0-1 seconds) within my epoched data and so on for varying time points (1-2 sec, 2-3sec, 3-4sec). This would allow me to have a useful table of information with comparative values, which I could then create comparative trend or bar graphs of different data sets that I have prepared.

If this is something that is already easily done in mne, I would very much appreciate a link or comment on this. Alternatively, if someone has some experience extracting and manipulating the data stored in .h5 files, I am sure your feedback would be helpful as well.

Thank you all for your time and assistance.

J

2

you should use https://mne.tools/stable/generated/mne.time_frequency.read_tfrs.html
to read such files

Alex

3

Thanks Alex. I have used the read_tfrs() function previously to generate tfr graphs as are done in the mne tutorials. I believe that my main problem is that I do not have experience working with hdf5 files and thus I am unfamiliar with how to properly extract the relevant information in the format that I need.

I’ve been reading more (Introduction to HDF5) and have explored my h5 files with HDFView, but I still am having issues understanding how the data is formatted.

Thank you for your comment though. If you have more thoughts, please do not hesitate to let me know.

4

after reading the tfr with read_tfrs you can have everything in the tfr object (data, channel names etc)

don’t try to reverse engineer the format. It’s done by the read_tfrs reader

Alex