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t1-linear - Affine registration of T1-weighted MR images to the MNI

standard space

This pipeline performs a set of steps in order to affinely align T1-weighted MR images to the MNI space using the ANTs software package [Avants et al., 2014]. These steps include: bias field correction using N4ITK [Tustison et al., 2010]; affine registration to the MNI152NLin2009cSym template [Fonov et al., 2011, 2009] in MNI space with the SyN algorithm [Avants et al., 2008]; cropping of the registered images to remove the background.

Tip

This pipeline can be also run with Clinica by typing clinica run t1-linear pipeline. Results are equivalent.

Dependencies

This pipeline needs the installation of ANTs on your computer. You can find how to install this software package on the third-party page on the Clinica Wiki.

Running the pipeline

The pipeline can be run with the following command line: 

clinicadl preprocessing run t1-linear <bids_directory> <caps_directory>
where:

  • bids_directory (str) is the input folder containing the dataset in a BIDS hierarchy.
  • caps_directory (str) is the output folder containing the results in a CAPS hierarchy.

On default, cropped images (matrix size 169×208×179, 1 mm isotropic voxels) are generated to reduce the computing power required when training deep learning models. Use --uncropped_image flag if you do not want to crop the image.

Tip

type clinicadl preprocessing run t1-linear --help to see the full list of parameters.

Outputs

Results are stored in the following folder of the CAPS hierarchy: subjects/sub-<participant_label>/ses-<session_label>/t1_linear with the following outputs:

  • <source_file>_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_T1w.nii.gz: T1w image affinely registered to the MNI152NLin2009cSym template and cropped.
  • (optional) <source_file>_space-MNI152NLin2009cSym_res-1x1x1_T1w.nii.gz: T1w image affinely registered to the MNI152NLin2009cSym template.
  • <source_file>_space-MNI152NLin2009cSym_res-1x1x1_affine.mat: affine transformation estimated with ANTs.

Warning

clinicadl preprocessing t1-linear is not deterministic. This variation comes from the third-party ANTS.