学习笔记44—Linux下安装freesurfer

时间:2024-01-19 23:36:50

第一步:安装ubuntu (略过)

第二步:下载freesurfer:从freesurfer的官方网站上下载:http://surfer.nmr.mgh.harvard.edu/fswiki/Download  ,此处下载的是freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

第三歩:安装freesurfer:

1)把freesurfer的安装包复制到 /usr/local;  在终端输入:cp  freesurfer所在位置  /usr/local

2) 进入 /usr/local,解压freesurfer文件,输入 sudo  tar -zxvf 文件名(如:sudo tar -zxvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz)

3) 安装tcsh (if not), 输入:sudo apt-get install tcsh;   完成后输入tcsh,不报错的话就没问题了。

4)配置环境变量:输入:sudo gedit  /etc/profile,在最后一行加入:export FREESURFER_HOME=/usr/local/freesurfer

5) sudo gedit  /etc/bash.bashrc  在最后一行加入:

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

6) 把注册时给的license文件复制到/usr/local/freesurfer里面

邮件内容如:

Here is your FreeSurfer license. Place the four lines between theCUT HERE markers in a file named "license.txt" in the directory pointed toby the $FREESURFER_HOME environment variable (see the FreeSurfer documentation).

#---------------CUT HERE---------------

xxxxxx

xxxxx

xxxxx

xxxxx

#---------------CUT HERE---------------

PS:如果未注册就点击:http://surfer.nmr.mgh.harvard.edu/registration.html

7)分别输入: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: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”

至此,大功告成!!!

其它:由于是ubuntu12.04的操作系统,所以可能会出现以下情况:“qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory”

解决方案:sudo ln -s /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 /usr/lib/libjpeg.so.62

reference:

1) http://52brain.com/forum.php?mod=viewthread&action=printable&tid=8723 (http://blog.sina.com.cn/s/blog_594168770101i52v.html)
2) http://wenku.baidu.com/link?url=86-qaV4F97xzdXtlFbXMztEyLij2Y6tTE5Zr5MY8I5lbKSPwRIpWWAcQ_ipLxRPLnknqeu5L9jR0xyuzAgaZq-EK7Jap7cdc8tBlC8OjVW3
3) https://blog.csdn.net/lj695242104/article/details/39988687
4)http://surfer.nmr.mgh.harvard.edu/registration.html