Cross-template warps (MNI152NLin6Asym ↔ MNI152NLin2009cAsym ↔ Colin27)

May 21, 2026 · View on GitHub

Overview

Inter-template warp fields for moving image data between the three MNI spaces commonly used in CANlab work — MNI152NLin6Asym (FSL default, also the canlab2024 grayordinate space), MNI152NLin2009cAsym (fmriprep default), and Colin27v1998 — in three software-native formats:

  • ants/ — ANTs .h5 composite transforms (use with antsApplyTransforms).
  • fsl/ — Equivalent affine + displacement-field pairs in FSL format (use with applywarp).
  • spm/ — Equivalent affine CSVs + SPM y-field deformations (use with spm_get_space / Normalise: Write, or the helper code/apply_spm_warp.m).

The original ANTs transforms were produced by running each template through fmriprep 20.2.3 with surface reconstruction enabled; a subcortically-weighted set (*_subctx_*) was generated with more aggressive SyN parameters and a cifti-volumetric mask metric for improved subcortical alignment, since the default fmriprep warps prioritise cortical correspondence. See code/README.md for the full methods narrative and example invocation lines for each toolchain.

A leads_dbs/ subfolder ships the Lead-DBS community's MNI152NLin6Asym <-> MNI152NLin2009bAsym warps (mass-univariate DBS-targeting use case) — see its README.txt and COPYING for provenance and licence.

download_warpfield.m is a one-line helper that fetches the large SPM y_* deformation files from figshare on demand, so the repository checkout itself can stay small.

Primary reference

Derived from publicly available MNI / Colin27 templates using fmriprep (ANTs SyN registration) as part of the CANlab build pipeline. For the underlying registration method see:

  • Avants, B. B., Epstein, C. L., Grossman, M., & Gee, J. C. (2008). Symmetric diffeomorphic image registration with cross-correlation. Medical Image Analysis, 12(1), 26–41. doi:10.1016/j.media.2007.06.004
  • Esteban O, Markiewicz CJ, Blair RW, et al. (2019). fMRIPrep: A robust preprocessing pipeline for functional MRI. Nature Methods, 16(1), 111–116. doi:10.1038/s41592-018-0235-9

How to use

ANTs (recommended — single resampling):

antsApplyTransforms -d 3 \
    -i input_MNI152NLin6Asym.nii.gz \
    -r MNI152NLin2009cAsym_T1_1mm.nii.gz \
    -t ants/MNI152NLin6Asym_to_MNI152NLin2009cAsym.h5 \
    -o output_in_fmriprep_space.nii.gz

FSL (apply both transforms at once — see code/README.md for premat ordering):

applywarp -i MNI152NLin6Asym_T1_1mm.nii.gz \
          -r MNI152NLin2009cAsym_T1_1mm.nii.gz \
          -o MNI152NLin6Asym_to_MNI152NLin2009cAsym_fsl.nii.gz \
          --premat=fsl/00_fsl_to_fmriprep_AffineTransform_mod.mat \
          -w     fsl/01_fsl_to_fmriprep_DisplacementFieldTransform_mod.nii.gz

SPM (MATLAB, via the helper code/apply_spm_warp.m):

apply_transforms('MNI152NLin2009cAsym_T1_1mm.nii', ...
                 'MNI152NLin6Asym_T1_1mm.nii', ...
                 [], ...
                 'spm/01_fmriprep_to_fsl_AffineTransform.csv', ...
                 'spm/y_00_fmriprep_to_fsl_DisplacementFieldTransform.nii', ...
                 'MNI152NLin2009cAsym_to_MNI152NLin6Asym_spm.nii', 1);

If the SPM y_* deformation files are not present locally:

download_warpfield('MNI152NLin6Asym', 'MNI152NLin2009cAsym', 'spm');

File inventory

File / dirWhat it is
ants/MNI152NLin6Asym_to_MNI152NLin2009cAsym.h5ANTs composite transform, FSL to fmriprep space.
ants/MNI152NLin2009cAsym_to_MNI152NLin6Asym.h5Inverse direction.
ants/MNI152NLin6Asym_to_MNI152NLin2009cAsym_subctx.h5Subcortically-weighted version (and inverse pair).
ants/MNI152NLin2009cAsym_to_MNI152NLin6Asym_subctx.h5Inverse subcortically-weighted.
ants/MNI152NLin6Asym_to_MNI152NLin2009bAsym.h5FSL to MNI152NLin2009bAsym (and inverse).
ants/MNI152NLin2009bAsym_to_MNI152NLin2009cAsym.h5Between 2009b and 2009c (and inverse).
ants/MNI152NLin6Asym_to_MNIColin27v1998.h5FSL to Colin27 (and inverse).
ants/MNI152NLin2009cAsym_to_MNIColin27v1998.h5fmriprep to Colin27 (and inverse).
ants/leads_dbs/Lead-DBS MNI152NLin6Asym <-> MNI152NLin2009bAsym warps (see README.txt, COPYING).
fsl/00_* / 01_* _AffineTransform_mod.mat / _DisplacementFieldTransform_mod.nii.gzFSL-format affine + warp pairs (cortical and _subctx).
spm/00_* / 01_* _AffineTransform.csvAffines as CSV for SPM.
spm/y_01_fsl_to_fmriprep_DisplacementFieldTransform.niiSPM y-field, FSL to fmriprep (cortical).
spm/y_01_fsl_to_fmriprep_subctx_DisplacementFieldTransform.niiSPM y-field, subcortically weighted.
spm/READMEExample invocation.
code/README.mdFull methods write-up + per-toolchain examples.
code/apply_spm_warp.mMATLAB helper to apply affine + y-field in one shot.
code/ea_antsmat2mat.mConvert ANTs affine to plain .mat.
code/ants_to_spm_warps.py, code/2_ants_to_spm_warps.pyConvert ANTs .h5 to SPM y-field.
code/fmriprep_to_fsl.sh, code/fsl_to_fmriprep.shPopulate the ants/ and fsl/ folders from a single .h5.
code/subctx_alignment.shBuilds the subcortically-weighted SyN.
code/0_populate_ants_and_convert_to_fsl.sh, code/1_ants_to_spm_mat.shDriver scripts.
download_warpfield.mFetches large SPM y-fields from figshare on demand.

Citations

  • Avants BB, Epstein CL, Grossman M, Gee JC (2008). Symmetric diffeomorphic image registration with cross-correlation. Med Image Anal 12:26–41. doi:10.1016/j.media.2007.06.004
  • Esteban O, Markiewicz CJ, Blair RW, et al. (2019). fMRIPrep: A robust preprocessing pipeline for functional MRI. Nat Methods 16:111–116. doi:10.1038/s41592-018-0235-9
  • Fonov VS, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL, Brain Development Cooperative Group (2011). Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54:313–327. doi:10.1016/j.neuroimage.2010.07.033
  • Holmes CJ, Hoge R, Collins L, Woods R, Toga AW, Evans AC (1998). Enhancement of MR images using registration for signal averaging. J Comput Assist Tomogr 22:324–333. doi:10.1097/00004728-199803000-00032
  • Lead-DBS warps: Horn A, Li N, Dembek TA, et al. (2019). Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging. NeuroImage 184:293–316. doi:10.1016/j.neuroimage.2018.08.068