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FreeSurfer segmentation
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
-wsthreshand-no-wsgcaatlasare 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.
