MNE_MRI_preprocessing

Before starting the Freesurfer analysis, you have to set some "environment variables", so that the following processing scripts know where to look for programs and data.

Type

freesurfer_4.3.0 and setenv SUBJECTS_DIR </myMRIdirectory/>

in your Linux command window.

Freesurfer will create a number of files in several subdirectories for each subject. You can automatically create the subdirecties for each subject

mksubjdirs <mysubjectname>

This will create the directory /myMRIdirectory/mysubjectname/, as well as several subdirectories. Check whether it worked, then forget about it for the time being. This is a good time to remind you that you will have to link each MRI data set with one MEG data set - you may therefore want to choose the names for your MRI subject directories wisely. If you link an MRI data set to the wrong MEG data set - well, you know what that means.

Convert your structural MRI image using

mri_convert </mridata/cbu/*/*/onedcmfile.dcm> </myMRIdirectory/mysubjectname/mri/orig/001.mgz>

You should specify one *.dcm-file for an MPRAGE MRI, which is usually located in a directory of the form /mridata/cbu/CBU123456_MR123456/123456_123456/Series_002_CBU_MPRAGE/1.2.3.4.1107.5.2.32.35119.123456123456.dcm. For example, choose the first or last dcm-file in the corresponding directory, the program will do the rest. The output directory .../mri/orig was created previously (remember, you've checked whether it worked...).