Miscellaneous C functionality

Setting up anatomical MR images for MRIlab

If you have the Neuromag software installed, the Neuromag MRI viewer, MRIlab, can be used to access the MRI slice data created by FreeSurfer . In addition, the Neuromag MRI directories can be used for storing the MEG/MRI coordinate transformations created with mne_analyze , see Coordinate frame alignment. During the computation of the forward solution, mne_do_forwand_solution searches for the MEG/MRI coordinate in the Neuromag MRI directories, see Computing the forward solution. The fif files created by mne_setup_mri can be loaded into Matlab with the fiff_read_mri function, see MNE-MATLAB toolbox.

These functions require running the script mne_setup_mri which requires that the subject is set with the --subject option or by the SUBJECT environment variable. The script processes one or more MRI data sets from $SUBJECTS_DIR/$SUBJECT/mri , by default they are T1 and brain. This default can be changed by specifying the sets by one or more --mri options.

The script creates the directories mri/ <name> -neuromag/slices and mri/ <name> -neuromag/sets . If the input data set is in COR format, mne_setup_mri makes symbolic links from the COR files in the directory mri/ <name> into mri/ <name> -neuromag/slices , and creates a corresponding fif file COR.fif in mri/ <name> -neuromag/sets .. This “description file” contains references to the actual MRI slices.

If the input MRI data are stored in the newer mgz format, the file created in the mri/ <name> -neuromag/sets directory will include the MRI pixel data as well. If available, the coordinate transformations to allow conversion between the MRI (surface RAS) coordinates and MNI and FreeSurfer Talairach coordinates are copied to the MRI description file. mne_setup_mri invokes mne_make_cor_set , described in mne_make_cor_set to convert the data.

For example:

mne_setup_mri --subject duck_donald --mri T1

This command processes the MRI data set T1 for subject duck_donald.


If the SUBJECT environment variable is set it is usually sufficient to run mne_setup_mri without any options.


If the name specified with the --mri option contains a slash, the MRI data are accessed from the directory specified and the SUBJECT and SUBJECTS_DIR environment variables as well as the --subject option are ignored.

MRIlab can also be used for coordinate frame alignment. Section 3.3.1 of the MRIlab User’s Guide, Neuromag P/N NM20419A-A contains a detailed description of this task. Employ the images in the set mri/T1-neuromag/sets/COR.fif for the alignment. Check the alignment carefully using the digitization data included in the measurement file as described in Section 5.3.1 of the above manual. Save the aligned description file in the same directory as the original description file without the alignment information but under a different name.

Cleaning the digital trigger channel

The calibration factor of the digital trigger channel used to be set to a value much smaller than one by the Neuromag data acquisition software. Especially to facilitate viewing of raw data in graph it is advisable to change the calibration factor to one. Furthermore, the eighth bit of the trigger word is coded incorrectly in the original raw files. Both problems can be corrected by saying:

mne_fix_stim14 <raw file>

More information about mne_fix_stim14 is available in mne_fix_stim14. It is recommended that this fix is included as the first raw data processing step. Note, however, the mne_browse_raw and mne_process_raw always sets the calibration factor to one internally.


If your data file was acquired on or after November 10, 2005 on the Martinos center Vectorview system, it is not necessary to use mne_fix_stim14 .

Fixing channel information

There are two potential discrepancies in the channel information which need to be fixed before proceeding:

  • EEG electrode locations may be incorrect if more than 60 EEG channels are acquired.
  • The magnetometer coil identifiers are not always correct.

These potential problems can be fixed with the utilities mne_check_eeg_locations and mne_fix_mag_coil_types, see mne_check_eeg_locations and mne_fix_mag_coil_types.