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We want to be able to project anatomical and functional volumes between the native and MNI spaces. fmriprep v1.0 uses ANTs v2.20 for registration. Here we describe how to download and compile ANTs v2.20 on your local computer. We will also make available the built binary on DropBox at:

Be sure to install git (http://git-scm.com/downloads) and cmake (http://www.cmake.org/cmake/resources/software.html) if you haven't done so already. Once you've done that, navigate to a directory which will contain the ANTs directory. Then "clone" the ANTs repository by typing $ git clone https://github.com/stnava/ANTs.git That will download the ANTs source code. What I do next is compile and install ANTs in a binary directory in the ANTs directory, i.e. $ cd ANTs $ mkdir bin Then you can configure and install, i.e. $ cd bin $ ccmake ../ You can change certain options, for example where to install ANTs. When you're finished, type 'c' for 'configure' and then 'g' for generating the makefile. Typing 'make' at the prompt should then produce the ANTs executables (including downloading and installation of ITK).

(Instructions taken from https://sourceforge.net/p/advants/discussion/840261/thread/18f0a686/)

Instructions for warping images using ANTS into MNI space

Warping the native T1 image to MNI anatomical space and resolution

• antsApplyTransforms -d 3 -o outputAnatRezFileName.nii.gz -v 1 -t mySubject_T1w_target-MNI152NLin2009cAsym_warp.h5 -i mySubject_T1w_preproc.nii.gz -r mySubject_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz

Warping the native T1 image to MNI functional space and resolution

• antsApplyTransforms -d 3 -o outputFuncRezFileName.nii.gz -v 1 -t mySubject_T1w_target-MNI152NLin2009cAsym_warp.h5 -i mySubject_T1w_preproc.nii.gz -r ../func/mySubject_myTaskAcquisition_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz

Adding ANTS to your path on Linux Open your bashrc file and add the following lines (~/.bashrc): export ANTSPATH=${HOME}/PATH_TO_ANTS_BIN_DIR == where this is the path to the compiled binary directory export PATH=${ANTSPATH}:$PATH == Append this the path restart your terminal test this by typing which antsRegistration