raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
Lets read the raw_fname
raw = mne.io.read_raw_fif(raw_fname, preload=True)
So now we can print the info by print(raw.info)
then we can see the name of the channel, but not the detailed info (coordinates, etc)
Please let me ask a question:
With brainstorm we can edit the channel file, explore it and clearly see the position and orientation of each channel, we can export it to matlab, and change what we want. With mne I dont know how. So I dont know if you know how in mne I can explore the fif file and change it, but as I am asking in brainstorm forum, so I would like to know how can I open the fif file, inorder to explore the channel and edit it? the above mentioned fif file seems to contains the channel information.
It depends on the dataset if the coordinates are in there. For some datasets, like EEG, it is not always in the file, because the montages differ so much from person to person. For MEG it could be in there. The .fif files are neuromag files, you could check on the internet how those files are built up and how to find things in them. Maybe the following MNE tutorial can help you with coordinates and sensors : https://mne.tools/dev/auto_tutorials/intro/plot_40_sensor_locations.html#sphx-glr-auto-tutorials-intro-plot-40-sensor-locations-py
In the link you share, they did not explain how to visualize the the coordinate and orientation of the sensors for meg like
(x y z for position)(a b c for orientation) and how can I alter them,?
you said It depends on the dataset if the coordinates are in there, yes the coordinates is in file, how can I open it with brainstorm?
As I face several problem in mne, I would like to open the dataset found there in mne, and work with it in Brainstorm, can you please explain for me step by step how to import all the fif file so that I creat the proper protocol with corresponding subject?
My apologies I didn't knew that you wanted to open the file in brainstorm. Reading in files in brainstorm is relatively easy. I would suggest you to go through the first set of tutorials on the tutorial page about reading in files, I think that would help you a lot in using the fif files https://neuroimage.usc.edu/brainstorm/Tutorials
@afo Indeed, if you're interested in using Brainstorm, our recommendation would be to follow step by step the introduction tutorials (section "Get started" in the Tutorials page), using the tutorial dataset. In the first seven tutorials, you'll find all the information you need regarding the import of data into Brainstorm and accessing the info in the Brainstorm database. https://neuroimage.usc.edu/brainstorm/Tutorials
After this basic training, in the section "Other analysis scenarios", you can find additional tutorials based on Elekta recordings (in FIF format).
After reading the tutorials, please let us know more precisely what information you could not find in the documentation and we'll be happy to help you.
For anything related with MNE, you should ask the MNE developers...
OK I will do, in the coil_def.mat there is Point magnetometer, can you please let me know which tutorial in BST deal with Point magnetometer? do you have a ready channel with Point magnetometer?
If you have a .fif file with a point magnetometer defined, the channel file would be created correctly with only one integration point.
If you create the channel.mat file manually, define the .Loc and .Orient field of each sensor with only one column (=one integration point).
Once your channel file is created and the data imported, everything would work exactly as presented in the tutorials, no matter how many coils or integration points you have in your sensors.
Thank you Francois,
In tutorial three they said I can export in one of the supported mesh file format by Right-click on a surface file, the right click did not work, and gives this message
With Brainstorm,-1) can we generate simulation of source with different orientation of dipole?
- 2) can we simulate patch source with group of dipoles?
And for the bug you're having, it's already fixed and the workaround for already imported data is described in this thread: Error visualization anatomy
Please create new threads for new questions and bug reports, it helps with the forum management and searches.
