Prerequisite

Anatomical MRI should have been acquired. The MRI sequence is described in the document on the right.

Goal of this tutorial

We will explain how to run a brain segmentation using FreeSurfer for source and head model design to analyse MEG data.

FreeSurfer finds interfaces between various brain structures (white & gray matter, gray and CSF...) and creates 3D models of these interfaces for later import in an MEG analysis software.

FreeSurfer Analysis Pipeline Overview is a good place to start tackling these steps (also useful info in the FAQ). Below is a minimalist setup guideline which should work at the CENIR for most subjects.

Step-by-step guide

Setup and run FreeSurfer

We set environment variables as follows.

$ export FREESURFER_HOME=/network/lustre/iss01/cenir/software/meeg/freesurfer/
$ export SUBJECTS_DIR=/network/lustre/iss01/cenir/analyse/meeg/YOUR_PROJECT/subjects
$ export SUBJECT=S01

We refer to these variables throughout this tutorial.

The segmentation program is called recon-all.

$ recon-all -i one_dicom_file_for_that_subject.MR.dic -all -qcache

This will run overnight. Come back tomorrow.

Results

Once computations are done, we need to check that the segmentation finished without error.

In the results folder ($SUBJECTS_DIR/$SUBJECT), there is a scripts directory and a file called recon-all-status.log.

This file should end with something similar to this:

#@# Qdec Cache rh w-g.pct.mgh fwhm20 fsaverage Sat Mar 25 02:33:49 CET 2017
#@# Qdec Cache rh w-g.pct.mgh fwhm25 fsaverage Sat Mar 25 02:33:54 CET 2017
#@# BA Labels lh Sat Mar 25 02:34:00 CET 2017
#@# BA Labels rh Sat Mar 25 02:37:42 CET 2017
#@# Ex-vivo Entorhinal Cortex Label lh Sat Mar 25 02:41:24 CET 2017
#@# Ex-vivo Entorhinal Cortex Label rh Sat Mar 25 02:41:36 CET 2017
recon-all -s S01 finished without error at Sat Mar 25 02:41:49 CET 2017

Important is the mention: finished without error .

Checking the results

Once the segmentation is done, we can view it with various tools:

Freeview

The simplest method is using Freeview. (you may need to install this library or a similar one)

$ source /network/lustre/iss01/cenir/software/irm/bin/source_sepproject.bash
$ fsViewPatient.py $SUBJECT

or

 $ fsViewPatient.py $SUBJECT -a

These are equivalent to the command:

 freeview -v ${SUBJECTS_DIR}/${subject}/mri/orig.mgz \
            ${SUBJECTS_DIR}/${subject}/mri/wm.mgz \
            ${SUBJECTS_DIR}/${subject}/mri/brainmask.mgz \
            ${SUBJECTS_DIR}/${subject}/mri/aparc+aseg.mgz \ # this line is added with the -a option above
         -f ${SUBJECTS_DIR}/${subject}/surf/lh.pial:edgecolor=red \
           -${SUBJECTS_DIR}/${subject}/surf/lh.white:edgecolor=blue \
           -${SUBJECTS_DIR}/${subject}/surf/rh.pial:edgecolor=red \
           -${SUBJECTS_DIR}/${subject}/surf/rh.white:edgecolor=blue

Which loads:

volumes (-v) orig.mgz, wm.mgz and brainmask.mgz
and surfaces (-f) pial surface in red, white-gray matter interface in blue
The aparc+aseg volume containing automated classification (labelling) of subcortical structuresChecking consists principally in verifying that surfaces are well aligned (non overlapping), and stick to the expected contrasts in the MRI.

If a problem appears, first check this page: TroubleshootingData.

Then there are usually two options:

Adjust parameters and restart the pipeline (entirely or in part). Options -wsthresh and -no-wsgcaatlas are worth your attention (SkullStripFix_freeview, also check the complete list of options: recon-all -help).
Editing brainmask by hand.

In any case, detailed information can be found at TroubleshootingData.

Tksurfer and Tkmedit

Another method uses tksurfer and tkmedit. Here are some of the possible checks, which should be adjusted to meet the specific needs of the user.

# checking surfaces
$ tksurfer $SUBJECT lh inflated
$ tksurfer $SUBJECT rh inflated
 
# check the talairach transform
tkregister2 --mgz --s $SUBJECT --fstal --surf orig
 
# check the skull strip
tkmedit $SUBJECT brainmask.mgz -aux T1.mgz -surfs
 
# check the white and pial surfaces
tkmedit $SUBJECT brainmask.mgz -aux wm.mgz -surfs
 
# check the segmentations
tkmedit $SUBJECT brainmask.mgz -surfs -aseg

For more detailed documentation (instructions, advice, examples): RecommendedReconstruction.
For details on manual editing of segmented surfaces: TkMeditSegmentations.

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