Install Softwares

Do it with for loop:

for sub in *;     do echo $sub;     3dSkullStrip -input ${sub}/T1_${sub}_S0001.nii -prefix ${sub}/T1_${sub}_S0001_3DSS.nii -mask_vol; done

for sub in *;     do echo $sub;     3dSkullStrip -input ${sub}/${sub}_3T_T1w_MPR1.nii -prefix ${sub}/${sub}_3T_T1w_MPR1_3DSS.nii -mask_vol;done

for sub in *;     do echo $sub;     3dSkullStrip -input ${sub}/T1_${sub}_V2.nii -prefix ${sub}/T1_${sub}_V2_3DSS.nii -mask_voldone

BEaST

*Done? Need to test.
- minc库位置 /opt/minc-itk4/lib
- beast-library-1.1位置 /opt/minc-itk4/share/beast-library-1.1

Usage:

1. $ source /opt/minc-itk4/minc-toolkit-config.sh2. PATH=$PATH:/opt/minc-itk4/bin

nii2mnc/opt/minc/bin/mincbeast /opt/minc/share/beast-library-1.0/ ~/Desktop/test.mnc ~/Desktop/output.mnc

return error

ERROR! Mask dimension does not match image dimension!

作者给的使用指南

---

ALFA

*下载需要填表格申请，等待中。。。
http://adni.loni.usc.edu/data-samples/access-data/

---

3dSkullStrip(3DSS in Afni)

https://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/linux_inst_basic.html
Error:

afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directoryUsage:

Fix:

# add to library pathecho 'export LD_LIBRARY_PATH="/usr/local/lib/:$LD_LIBRARY_PATH"' >> ~/.bashrc. ~/.bashrc

Usage:

3dSkullStrip -input inputfile -prefix outputfile -mask_vol

Something to keep in mind:
-mask_vol: Output a mask volume instead of a skull-stripped
volume.
The mask volume containes:
0: Voxel outside surface
1: Voxel just outside the surface. This means the voxel
center is outside the surface but inside the
bounding box of a triangle in the mesh.
2: Voxel intersects the surface (a triangle), but center
lies outside.
3: Voxel contains a surface node.
4: Voxel intersects the surface (a triangle), center lies
inside surface.
5: Voxel just inside the surface. This means the voxel
center is inside the surface and inside the
bounding box of a triangle in the mesh.
6: Voxel inside the surface.

---

BET(in FSL)

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide
Usage:

bet inputfile outputfile -m

---

BSE

*Done
http://forums.brainsuite.org/download/

• Unzip and untar BrainSuite14c.linux.tar.gz file.This will create a BrainSuite14c folder which includes the files for BDP and SVReg.
• As the GUI hasn’t been released yet for Linux, both BDP and SVReg have to be run as command-line programs. You can invoke BDP and SVReg with their full path (e.g. ~\BrainSuite14c\bdp\bdp.sh <arguments>) from the terminal.
  Usage:

 /home/usrname/Downloads/BrainSuite15c/bin/bse <arguments>

---

LABEL(ibeat)

*Done
http://www.nitrc.org/frs/?group_id=574
Usage:

 export IBEAT_HOME=~/programs/ibeat $IBEAT_HOME/ibeatEnv.bash ibeat

---

ROBEX

*Done
Usage:

/home/usrname/Downloads/ROBEX/runROBEX.sh inputFile strippedFile [outputMaskFile] [seed]

---

Majority Vote(MV)

*Last step “make” error: skipping incompatible

# IRTK Installation## Dependencies1. IRTK requires the following:     - [FLTK](http://www.fltk.org/) library.         - Version 1.3 has been tested and is recommended.          - export FLTK_DIR=/home/kp2644/Downloads/fltk-1.3.3     - [VTK 5 or 6](http://www.vtk.org/) library.     - [Boost](http://www.boost.org/) library.         - Not a version earlier than 1.48.         - export BOOST_ROOT=/home/kp2644/Downloads/boost_1_61_0/     - The [GNU Scientific Library](http://www.gnu.org/software/gsl/) is also essential.2. You will also need to have [CMake](http://www.cmake.org/) installed, in order to generate the native build environment.## RequirementsThe applications of the IRTK can be run on Linux distributionsand Mac OS X. On Windows, [Cygwin](https://www.cygwin.com/) must be installed first.## Build and Installation1. Clone the repository    ```shell    git clone --recurse-submodules https://github.com/BioMedIA/IRTK.git IRTK    cd IRTK    ```2. Create a build directory and change to the build directory    ```shell    mkdir build    cd build    ```3. Build IRTK.    You can configure IRTK with BUILD_TEST option set to ON using [CMake](http://www.cmake.org/cmake/help/runningcmake.html)    and build the software using the selected build tool (e.g., [GNU Make](http://www.gnu.org/software/make/)) to build the tests.    ```shell    cmake ..    make    ```## ConfigurationAdd the directory containing the IRTK binaries to your **PATH** environment variable.[GNU Bash](http://www.gnu.org/software/bash/):```bashexport PATH="$IRTK_DIR/bin:$PATH"<div class="se-preview-section-delimiter"></div>

C shell:

setenv PATH "$IRTK_DIR/bin:$PATH"<div class="se-preview-section-delimiter"></div>

where IRTK_DIR is the path to the IRTK build or installation directory.
“`

---

STAPLE

*Done
http://www.itksnap.org/download/snap/process.php?link=7962&root=nitrc
Usage:
Just go to /home/usrname/Downloads/itksnap-3.4.0-20151130-Linux-x86_64/bin, and double click ‘itksnap’

---

Shape-based Averaging(SBA)

*Need dcmtk, but dcmtk can only be installed using binaries, and rpm file of cmtk can’t find it.

---

Brainwash(BW)

*./brainwash: error while loading shared libraries: libz.so.1: wrong ELF class: ELFCLASS64

---

MASS

*Failed building wheel for scikit-learn
*C++源代码，要compile，install说明文件夹里有
https://www.cbica.upenn.edu/sbia/software/
DRAMMS:/opt/sbia/dramms-1.4.2
BASIS not finished

Many other segmentation methods on this web.