Skip to content

README.md

Latest commit

 

History

History
96 lines (68 loc) · 3.57 KB

README.md

File metadata and controls

96 lines (68 loc) · 3.57 KB

Templates

Reference T1-weighted templates in common MNI / stereotactic spaces. These are the canonical target spaces that atlases and signatures in this repo are aligned to. Different software packages and atlas builds use different MNI templates — collect them here so you can verify alignments at a glance and use the right one for your pipeline.

Although all data provided by Neuroimaging Pattern Masks should be in MNI space, different reference templates may have been used for spatial normalisation for generating specific atlases and maps. This is probably not consistently documented, but some common templates are provided here for those cases in which the standard- space template is described.

For a helpful discussion of MNI templates, see lead-dbs.org / About the MNI spaces. Most official MNI atlases are at nist.mni.mcgill.ca/atlases, and the BIDS coordinate-systems table is a useful cross-reference of which software uses which template.

Naming convention: <ref_space>_<modality>_<resolution>.<extension>.

Templates included

HCP / FSL

HCP and current FSL use the asymmetric MNI152 nonlinear 6th-generation template — MNI152NLin6Asym. Originally distributed via HCPpipelines/global/templates.

  • MNI152NLin6Asym_T1_1mm.nii.gz
  • MNI152NLin6Asym_T1_2mm.nii.gz

You can confirm FSL still tracks this build by checking that $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz matches the 2 mm file above.

fMRIPrep / QSIPrep

MNI152NLin2009cAsym (used by fMRIPrep and QSIPrep). Atlases destined for these preprocessing pipelines should be in this space.

  • MNI152NLin2009cAsym_T1_1mm.nii.gz
  • MNI152NLin2009cAsym_T1_2mm.nii.gz
  • MNI152NLin2009cAsym_T1_1mm_brainmask.nii.gz — brain mask.
  • MNI152NLin2009cAsym_1mm_t1s_lps.nii.gz — same volume in LPS orientation.
  • MNI152NLin2009bAsym_T1_0.5mm.README — note on the 2009b variant.

Pulled from the TemplateFlow repo.

SPM12

SPM12 uses a slightly modified MNI152 linear template, distributed as canonical/avg152T1.nii in SPM and provided here for SPM-derivative work outside of SPM:

  • IXI549Space_T1_2mm.nii.gz

SPM99–SPM8

These use MNI152Lin. Source: bic.mni.mcgill.ca / ICBM152Lin.

  • MNI152Lin_T1_1mm.nii.gz

SPM96 / BioImage Suite

MNIColin27 — a single-subject template (Colin scanned 27 times, co-registered and averaged). High detail but less representative. Used when extreme spatial detail is needed (e.g., histology registration). Source: nist.mni.mcgill.ca / Colin 27 average brain.

  • MNIColin27_T1_1mm.nii.gz

This is the 1998 version; the 2008 version has slightly different geometry.

Sub-folders

Folder Description
cerebellum Cerebellar atlas / template resources.
transforms Cross-template transforms (e.g., MNI152NLin6Asym ↔ MNI152NLin2009cAsym).

Contributing

Add any template you find useful here, with a comment in this document on when to use it. The reference template, spatial resolution, and imaging modality should be clear from the filename.

— Bogdan Petre, 10/10/23 (extended into landing-page form here).