I am trying to plot the co-registration of the sensors, the headmodel and compute a source model for the HCP data after extracting the data using MNE-HCP, however, it is a bit complicated because it seems like the HCP output is defined in a different coordinate system from MNE.
I just read through the tutorial you sent me last Friday: How MNE uses FreeSurfer’s outputs — MNE 0.24.1 documentation
If I understand correctly, all the analysis of MNE are based on the MRI surface RAS coordinate system that FreeSurfer uses. If I want to run source localization, I will need the sensor data, the headmodel and the source cortical surface/volume grid all align to the same coordinate system, in this case, the (FreeSurfer) MRI Surface Coordinate system.
My first question is related to the “convert” parameter in the “mne.io.read_raw_bti” function. The HCP data is originally collected using a “Magnes 3600wh” system, and MNE-HCP is using the “mne.io.read_raw_bti” to read in the BTi/4D data. The “covert” parameter, which is set to “False” in MNE-HCP, forces the data to covert to a Neuromag coordinate. I think this is why the orientation of the sensors are rotated in the psd plot, because MNE-HCP does not convert the coordinates to Neuromag. I am still not sure why this is turned off in MNE-HCP, it says in the documentation that there is a compatibility issue between HCP and MNE is terms of the coordinate systems (mne-hcp/read.py at 7dc789f44033e9b57f875da5794202e3a5290971 · mne-tools/mne-hcp · GitHub). According to this page in Fieldtrip (How are the different head and MRI coordinate systems defined? - FieldTrip toolbox), the BTi/4D data is in a ALS orientation. Is there a reason why this is by default converted to Neuromag? It also seems like the Neuromag data is not defined in the FreeSurfer coordinate system that MNE desires. After loading the data into MNE and converted to Neuromag, do I need to transform the sensors to the MRI Surface RAS for source localization?
Second, The MNE-HCP also loaded the headmodel generated by the HCP pipeline. However, I can almost be sure that the headmodel in the HCP output is not define in the MRI Surface RAS coordinate. I am assuming if HCP used FreeSurfer for the reconstruction, we should be able to find a transformation file that converts the headmodel to the FreeSurfer coordinate (MRI Sruface RAS coordinate), which can be co-registered to the sensors and then calculate the forward and inverse solution, correct?
The third question is more related to computing the source, surface-based or volumetric. According to this (Head model and forward computation — MNE 0.24.1 documentation), in order to calculate the source space, I need to have the FreeSurfer reconstruction output for the cortical surface. Can I assume that the source points generated from the FreeSurfer recon output is automatically defined in the MRI Surface RAS coordinate?
It is quite long, but I am trying to bridge the gap between HCP and MNE. Please let me know if you know the answers to these questions. Thank you!
Best,