Neuro Software | Greydon Gilmore

ANTs (Advanced Normalization Tools) Install

Mon, 28 Sep 2020 00:00:00 +0000

Get the latest ANTs code

You will need to install the ZLIB libraries:

sudo apt install zlib1g-dev

Obtain the newest version of ANTs by running the following:

mkdir -p ~/Documents/code/ants_source
cd ~/Documents/code/ants_source
git clone https://github.com/ANTsX/ANTs.git .

Run CMake/Make

Make the build directory.

The default install location is /opt/ANTs, which falls on your PATH. This is the easiest location to install. If you want to install somewhere else then specify the path in the CMAKE_INSTALL_PREFIX variable.

mkdir -p ~/bin/ants
cd ~/bin/ants
ccmake ~/Documents/code/ants_source

Hit ‘c’ to do an initial configuration. CMAKE will do some checking and then present options for review. Hit ‘c’ again to do another round of configuration. If there are no errors, you’re ready to generate the make files by pressing ‘g’.

Now you are back at the command line, it’s time to compile:

make -j

cd ~/bin/ants/ANTS-build
sudo make install

Post-install Configuration

You will need to edit your .bashrc or .zshrc file by adding the following lines:

export PATH=$PATH:/opt/ANTs/bin

Now check this worked correctly:

which antsRegistration

NiftyReg Install

Sun, 28 Jun 2020 00:00:00 +0000

Download NiftyReg

Obtain the newest version of NiftyReg or by running the following:

mkdir -p ~/Documents/code/niftyreg_source
cd ~/Documents/code/niftyreg_source
git clone https://github.com/SuperElastix/niftyreg.git .

Run CMake/Make

Make the build directory.

The default install location is /usr/local, which falls on your PATH. This is the easiest location to install. If you want to install somwhere else then specify the path in the CMAKE_INSTALL_PREFIX variable.

mkdir -p ~/bin/niftyreg
cd ~/bin/niftyreg
ccmake ~/Documents/code/niftyreg_source

The following options will be displayed, ensure you change CMAKE_INSTALL_PREFIX variable to the install directory path if you don’t want to use default:

To avoid compiling errors, turn USE_OPENMP OFF.

Parameter	Value
BUILD_ALL_DEP	Set to ON if you want to build All the dependencies
BUILD_SHARED_LIBS	Build the libraries as shared build the libraries as shared
BUILD_TESTING	Set to ON if you want to build the unit tests
CMAKE_BUILD_TYPE	Compiling options: Debug Release RelWithDebInfo MinSizeRel
CMAKE_INSTALL_PREFIX	Set the path where the final install will be copied
M_LIBRARY	Path to a library.
PNG_INCLUDE_DIR	Set if you want NiftyReg to support the PNG file format for 2D images. Note that CMake will try to find the libpng on your system and will build it automatically if it does not find it.
USE_CUDA	Set to ON if you want to build the GPU code. The CUDA toolkit must be install otherwise CMake will return an error message
USE_OPENCL	Set to ON to use OpenCL for multi-CPU implementation.
USE_OPENMP	Set to ON to use OpenMP for multi-CPU implementation.
USE_SSE	Set to ON to use SIMD based implementation, mostly for cubic B-Spline related computation. Note that SIMD implementation has only be done for single precision.

Press ‘c’ to configure the NiftyReg project, press ‘c’ to configure the project. Once the project is correctly configured, press the ‘g’ key to generate the Makefiles. You can then build and install the project:

sudo make -j
sudo make install

Post-Install Configuration

The project should then be installed into the CMAKE_INSTALL_PREFIX directory you previously created.

If you changed the install prefix directory, to one not on your PATH, you will need to add NiftyReg to your PATH. In order to use NiftyReg in any terminal, you will need to edit your .bashrc or .profile file by adding the following lines:

NREG=<path_to_your_niftyreg_install>
export PATH=$PATH:$NREG/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NREG/lib

Close and re-open the linux terminal then run:

reg_f3d

FSL (FMRIB Software Library) Install

Mon, 28 Oct 2019 00:00:00 +0000

Installing on Pop_OS!

You will first need to run the following steps prior to installing FSL.

The following steps were originally written here here .

Make sure you run a backup prior to performing this hack… just in case.

move your current OS information files into a temporary location:

sudo mv /etc/os-release /etc/os-release.pop && sudo mv /etc/lsb-release /etc/lsb-release.pop

write a new os-release file:

sudo gedit /etc/os-release

copy the following into this file:

NAME="Ubuntu"
VERSION="20.04 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

write a new lsb-release file:

sudo gedit /etc/lsb-release

copy the following into this file:

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04 LTS"

now run the fslinstaller.py script in the below section and return here to Step 5 to return your OS information.
after running the FSL install steps, remove the files you wrote:
```
sudo rm /etc/os-release && sudo rm /etc/lsb-release
```

move the original files back:

sudo mv /etc/os-release.pop /etc/os-release && sudo mv /etc/lsb-release.pop /etc/lsb-release

Download FSL

The easiest method is to download this python script.

You will need to register. On the subsequent page you will download the fslinstaller.py file.

Run the following in a linux terminal (the install will take awhile):

python /mnt/c/Users/*[your_username]*/Downloads/fslinstaller.py

You will also need to install the package wxpython:

pip install wxpython

If that does not work then run:

pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-16.04 wxPython

Libraries you may need to install

Multiple-image Network Graphics library (libmng)

sudo apt-get install libmng2
sudo apt-get install libmng-dev

PNG library - development (libpng-dev)

sudo apt-get install libpng-dev

Optimized BLAS (linear algebra) library (libopenblas-base)

sudo apt-get install libopenblas-base
export LD_LIBRARY_PATH=/usr/lib/openblas-base/

libmng.so.1 Error

You will need to create a symbolic link for the library dll libmng.so.1:

sudo ln -s /usr/lib/x86_64-linux-gnu/libmng.so.2 /usr/lib/x86_64-linux-gnu/libmng.so.1

Independent JPEG Group’s JPEG runtime library (libjpeg62)

sudo apt-get install libjpeg62

PNG library - runtime (libpng12.deb)

wget -q -O /tmp/libpng12.deb http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb \
&& sudo dpkg -i /tmp/libpng12.deb \
&& rm /tmp/libpng12.deb

GTK+ graphical user interface library (gtk2.0)

sudo apt-get install gtk2.0

Pulseaudio for other random libraries

sudo apt-get install pulseaudio

You may also receive an error `No D-BUS daemon running`, run the following:

sudo chown -R *[your username]*:admin ~/.dbus

ART (Automatic Registration Toolbox) Install

Thu, 28 Jun 2018 00:00:00 +0000

Download ART

Download the newest version of ART

Make a new directory for the install and extract the tar package into it:

mkdir ~/Applications/ART
cd ~/Applications/ART
tar -xvzf /mnt/c/Users/*[your_username]*/Downloads/acpcdetect2.0*.tar.gz

Post Configuration

Set the ARTHOME environment variable and add the binary directory to your PATH by editing your ~/.bashrc file:

vim ~/.basrc

Add these lines to the end:

export ARTHOME=/path/to/ART
export PATH=$ARTHOME/bin:$PATH

Confirm Installation

Execute acpcdetect by running command in terminal

You may get an error when executing acpcdetect:

acpcdetect: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory

If you get this error, run the following:

sudo apt-get install libatlas-base-dev

You will also need to install pnmtopng

sudo apt-get install -y pnmtopng

Make and CMake Install

Thu, 28 Jun 2018 00:00:00 +0000

Install Make

Install build essentials and Make first:

sudo apt-get install make
sudo apt-get update && sudo apt-get install build-essential

Install CMake

Download the latest version of the CMake executable.

In your linux shell run (replacing VERSION with the version you downloaded):

VERSION=4.1.1
cd ~/Downloads
chmod +x cmake-$VERSION-linux-x86_64.sh
sudo ./cmake-$VERSION-linux-x86_64.sh
sudo mv cmake-$VERSION-linux-x86_64 ~/bin/cmake

Then add the following line to your .basrc or .zshrc, replacing the path with the path to cmake install on your system:

export PATH=$PATH:$HOME/bin/cmake/bin

Dcm2niix Install

Sun, 28 May 2017 00:00:00 +0000

Run Install

Run the following code in a linux terminal:

sudo apt-get install dcm2niix

Install Dependencies

There are a few packages that allow dcm2niix to run faster:

sudo apt-get install python-gdcm
sudo apt-get install pigz

Freesurfer Installation

Mon, 01 Jan 0001 00:00:00 +0000

Download software

Download the .deb file for Freesurfer.

Run the following command (replacing the filename with the one you downloaded):

cd ~/Downloads
sudo dpkg -i freesurfer_ubuntu22-8.1.0_amd64.deb

You will also need to install some dependancies:

sudo apt-get install tcsh
sudo apt-get install libglu1
sudo apt-get install libxss1

Post-Install Configurations

Add Freesurfer to your path:

echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc
echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc

If you have run the install correctly you will see this output when you close and open a new terminal window:

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni

Define subjects_dir

FreeSurfer requires an environment variable called SUBJECTS_DIR. This is the directory where subject data is stored, put this in your ~/.bashrc or ~/.zshrc:

export SUBJECTS_DIR=<path to subject data>

Obtain license

You will need to obtain a license key.

Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable.

sudo mv ~/Downloads/license.txt $FREESURFER_HOME

Neuro Software | Greydon Gilmore

ANTs (Advanced Normalization Tools) Install

Get the latest ANTs code

Run CMake/Make

Post-install Configuration

NiftyReg Install

Download NiftyReg

Run CMake/Make

Post-Install Configuration

FSL (FMRIB Software Library) Install

Installing on Pop_OS!

Download FSL

Libraries you may need to install

Multiple-image Network Graphics library (libmng)

PNG library - development (libpng-dev)

Optimized BLAS (linear algebra) library (libopenblas-base)

libmng.so.1 Error

Independent JPEG Group’s JPEG runtime library (libjpeg62)

PNG library - runtime (libpng12.deb)

GTK+ graphical user interface library (gtk2.0)

Pulseaudio for other random libraries

You may also receive an error No D-BUS daemon running, run the following:

ART (Automatic Registration Toolbox) Install

Download ART

Post Configuration

Confirm Installation

Make and CMake Install

Install Make

Install CMake

Dcm2niix Install

Run Install

Install Dependencies

Freesurfer Installation

Download software

Post-Install Configurations

Define subjects_dir

Obtain license

You may also receive an error `No D-BUS daemon running`, run the following: