Hello MNE users
Some time ago I asked questions about phase-locking value analysis with MNE, and this e-mail is also related to that topic.
For the proposed single-trial procedures, the labels used need to be in subject-specific cortical space, so each label needs to be morphed onto the subjects own cortex (mne_morph_labels).
This worked well when I need to export an average waveform from my label.
Now my problem is when I want to export each vertices from a specific label.
Because the label is on subject-specific cortical space, I do not have the same number of vertices extracted for the label of interest for each subject.
To create a group average I need to find a way to have this data transform into an average-brain but so far, I am failing to find the solution in the manual. The only brain morph option that is explained in the manual is about evoked data (mne_make_movie) and not raw or epochs data.
I will be grateful to hear about any solution to resolve this.
Thanks in advance for your help
Elisabeth
Hi Elisabeth,
Not sure if I understood the question correctly... You want to invert
raw epochs of data in the subject space and morph that to the average
brain?
If that is indeed the case, one way it can be done is partly in MATLAB
using mne_ex_read_epochs() and mne_ex_compute_inverse() that come with
the MNE suite. One can use those results to make stc files using another
MATLAB function: mne_write_stc_files(). The morphing can now be done
with mne_make_movie using the --stcin, --morph and --stcout options.
Hope that helps.
Regards,
Hari
You can also "trick" the MNE suite by creating an average fif file that has a single trial of the length of your entire run. Then you can just use mne_make_movie to make the stc file from there using the inverse operator and the "average" fif file.
That said, if I understand what you want to do, a much easier approach is to draw your label on the average brain, then project that label back onto each individual using freesurfer. Then you have a label on each individual which is anatomically relatively identical across subjects. This should behave the same as if you had morphed each individual's raw data onto the average brain and extracted the vertices from that ROI.
Hi Elisabeth,
Not sure if I understood the question correctly... You want to invert
raw epochs of data in the subject space and morph that to the average
brain?
If that is indeed the case, one way it can be done is partly in MATLAB
using mne_ex_read_epochs() and mne_ex_compute_inverse() that come with
the MNE suite. One can use those results to make stc files using another
MATLAB function: mne_write_stc_files(). The morphing can now be done
with mne_make_movie using the --stcin, --morph and --stcout options.
Hope that helps.
Regards,
Hari