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| 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. | == Creating the environment == The processing steps are required for MNE, but they are actually performed in Freesurfer. 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. |
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| == Reconstruction == |
MNE_MRI_preprocessing
Creating the environment
The processing steps are required for MNE, but they are actually performed in Freesurfer. 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...).
Reconstruction
The next three steps are the ones that do the important stuff. You can run them one after the other and hope for the best. But it is recommended to check the result of each step, and rerun the analysis if necessary.
recon-all -subjid <mysubjectname> -autorecon1
Check the result of autorecon1.
recon-all -subjid <mysubjectname> -autorecon2 Check the result of autorecon2.
recon-all -subjid <mysubjectname> -autorecon3 Check the result of autorecon3.