MneExperiment analysis options

Table of Contents

• Empty room covariance
• Analysis without baseline correction
• Multiple visits

Empty room covariance

• Put an empty room recording in each subject’s MEG directory, just like the other MEG files, with session name “emptyroom”. If you want to use the same empty room file for all subjects you can make links instead of copies to save space.

• Add “emptyroom” as a session to the experiment definition.

• Use the empty room covariance with e.set(cov=‘emptyroom’)

Analysis without baseline correction

Epochs always have a baseline time window in their specification. However, whether this window is used or not depends on the test parameters: for example, most source space analyses can be performed without baseline correction by specifying baseline=False in the relevant MneExperiment method. The baseline is always used for computation of the sensor noise covariance matrix, so a reasonable baseline should be set for the cov epoch.

Multiple visits

Multiple MEG recording files for the same subject can be designated with different session names. However, when subjects leave the MEG device and come back for a new recording on a different day, an additional visit setting is necessary. What necessitates this additional setting is that the different visits usually require separate head-MEG coregistration files. Technically, whenever the head shape recording (recorded with the head digitizer pen or scanner) is different for two recordings, a separate coregistration is required.

In order to implement different visits in the MneExperiment pipeline:

• Add a visits attribute to the MneExperiment subclass definition, with a list of visit names. The empty string is allowed. For example, for a base recording and a 6 month follow up, you could use visits = (‘’, ‘6mt’).

• For MEG FIFF files, the {session} template is extended to {session} {visit}. When visit is ’’, it is just {session}. In the example, if the recording session is called “task_1”, you would have two FIFF files for each subject, Rxxx_task_1-raw.fif and Rxxx_task_1 6mt-raw.fif.

• Each visit needs a separate coregistration. These would be Rxxx-trans.fif and Rxxx 6mt-trans.fif.

  • When using a template brain: since the participant’s head size should not change between visits, use the same MRI-subject for all visits. From the second visit onwards, do coregistration as if an actual MRI were available: select the previously scaled MRI as MRI subject, and set Scaling mode to None. When hitting Save, you should only be prompted to save a *-trans.fif-file, without creating a separate MRI-subject.

visit now is an analysis parameter. Use e.set(visit=‘’) and e.set(visit=‘6mt’) to perform preprocessing and data analysis for the different visits.