如何做一个常规的Freesurfer脑部核团分析

1 FreeSurfer安装

tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

if in Ubuntu system, a few external packages are required.
On Ubuntu:
apt-get -y install bc binutils libgomp1 perl psmisc sudo tar tcsh unzip uuid-dev vim-common libjpeg62-dev

2 初始设置

Linux:

## bash
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh 


3 SUBJECTS_DIR (location of subject data)
## bash
export SUBJECTS_DIR=<path to subject data> 

4 测试FreeSurfer安装

Example 1: Convert the sample-001.mgz to nifti format. 

cp $FREESURFER_HOME/subjects/sample-001.mgz .
mri_convert sample-001.mgz sample-001.nii.gz 


Example 2: Perform a full recon-all on the nifti file. 

export SUBJECTS_DIR=<path to subject directory>
recon-all -i sub_01.nii.gz -s bert -all (creates a folder called bert
in SUBJECTS_DIR)
a
Example 3: Perform a full recon-all on a pre-existing subject folder

export SUBJECTS_DIR=<path to subject directory>
recon-all -s bert -all

Example 4: View the output volumes, surfaces and subcortical segmentation of the fully recon-ed
subject bert. 

cd $SUBJECTS_DIR
freeview -v \
 bert/mri/T1.mgz \
 bert/mri/wm.mgz \
 bert/mri/brainmask.mgz \
 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
 -f \
 bert/surf/lh.white:edgecolor=blue \
 bert/surf/lh.pial:edgecolor=red \
 bert/surf/rh.white:edgecolor=blue \
 bert/surf/rh.pial:edgecolor=red

在原始空间提取特17,53两个脑区作为脑模板

mri_extract_label aseg.mgz 17 53 hippo_mask.mgz

mri_convert T1.mgz T1.nii.gz 

多个病例同时重建

export SUBJECTS_DIR=`pwd`

ls *.nii.gz | parallel --jobs 11 recon-all -s {.} -i {} -all -qcache



Command 'parallel' not found, but can be installed with:

sudo apt install moreutils
sudo apt install parallel 

提取多个脑区作为脑模板

asegstats2table --subjects 01 02 03 04 05 06 07 08 09 10 11 \
--segno 11 17 18 \
--tablefile aseg.vol.table