Freesurfer目前只支持安装在Linux系统上
这里写目录标题
FreeSurfer安装步骤
https://blog.csdn.net/zuzhiang/article/details/107562854
安装在自己的虚拟环境里面即可:
(1)将压缩包放在/home/tj/application/里面
(2)运行命令 解压压缩包 当前路径:sudo tar -zxvf freesurfer安装包文件名
(3)改变freesurfer的文件权限:sudo chmod -R 777 ./freesurfer
(4)配置全局环境变量:sudo gedit /etc/profile(到这一步了)
export FREESURFER_HOME=/usr/local/freesurfer
(5)配置当前用户环境变量:sudo gedit /etc/bash.bashrc
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FREESURFER_HOME=/home/lxw/Freesurfer/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
(6)将注册的license文件复制/application/freesurfer/
sudo cp /home/tj/application/license.txt /home/tj/application/freesurfer
(7)分别输入:
分别输入帮助指令:tkregister2、tkmedit、tksurfer 和recon-all --help没有报错的话 就说明基本安装成功了。
(8)输入如下指令( Perform a full recon-all on a pre-existing subject folder),验证是否成功
recon-all -s bert -autorecon1
等一段时间,出现“recon-all -s bert finished without error at Sat Oct 11 10:07:49 CST 2014 done”
FreeSurfer配准步骤
如果对命令不熟悉,那么可以使用help来查看,或者区官网看更详细的介绍
(1)rh.thickness
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/thickness --trg_type curv --hemi lh
mri_surf2surf --srcsubject /3.11/HLN-12-2 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/student8/application/freesurfer/subjects/3.11/mintemplate/HLN/thickness --trg_type curv --hemi lh
(2)rh.area
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval area --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/area --trg_type curv --hemi lh
(3)rh.sulc
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval sulc --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/sulc --trg_type curv --hemi lh
(4)rh.curv
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval curv --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/curv --trg_type curv --hemi lh
(5)rh.volume
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval volume --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/volume --trg_type curv --hemi lh
(6)雅克比度(rh.jacobian_white)
mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval jacobian_white --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/jacobian_white --trg_type curv --hemi lh
(7)rh.white
mri_surf2surf --s OASIS-TRT-20-1 --hemi lh --sval-tal-xyz white --trgsubject fsaverage5 --tval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/lh.white --tval-xyz $SUBJECTS_DIR/fsaverage5/mri/orig.mgz
(8)rh.annotation
mri_surf2surf --srcsubject OASIS-TRT-20-1 --trgsubject fsaverage5 --hemi lh --sval-annot /home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/label/lh.labels.DKT31.manual.annot --tval /home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/lh.labels.DKT31.manual.annot