AMU7T : high-resolution multimodal quantitative T1 and T2*-weighted templates with white and gray matter spinal cord and substructures atlas, aligned with the PAM50 space
This data repository contains:
template/AMU26_qt1.nii.gz: 7T qT1 template from 26 subjects.template/AMU72_t2s.nii.gz: 7T T2*w template from 72 subjects.template/AMU7T_gm.nii.gz: Probabilistic gray matter mask.template/AMU7T_wm.nii.gz: Probabilistic white matter mask.template/AMU7T_sc.nii.gz: Probabilistic spinal cord mask.atlas/AMU7T_50_labels.nii.gz: Atlas with 50 labels (WM parcels from Lévy et al., NeuroImage (2015)., and GM parcels derivated from Hausman, L. Atlases of the Spinal Cord and Brainstem and the Forebrain. (Thomas, 1962).atlas/AMU7T_label_ID_bin.nii.gz: Binary masks by ID.
Multilabel atlas in in atlas/AMU7T_50_labels.nii.gz containing:
ID (compatible with PAM50 ID) - Name
- 0 - WM Left fasciculus-gracilis
- 1 - WM Right fasciculus-gracilis
- 2 - WM Left fasciculus-cuneatus
- 3 - WM Right fasciculus-cuneatus
- 4 - WM Left lateral-corticospinal-tract
- 5 - WM Right lateral-corticospinal-tract
- 6 - WM Left ventral-spinocerebellar-tract
- 7 - WM Right ventral-spinocerebellar-tract
- 8 - WM Left rubrospinal-tract
- 9 - WM Right rubrospinal-tract
- 10 - WM Left lateral-reticulospinal-tract
- 11 - WM Right lateral-reticulospinal-tract
- 12 - WM Left spinal-lemniscus-spinothalamic
- 13 - WM Right spinal-lemniscus-spinothalamic
- 14 - WM Left spino-olivary-tract
- 15 - WM Right spino-olivary-tract
- 16 - WM Left ventrolateral-reticulospinal-tract
- 17 - WM Right ventrolateral-reticulospinal-tract
- 18 - WM Left lateral-vestibulospinal-tract
- 19 - WM Right lateral-vestibulospinal-tract
- 20 - WM Left ventral-reticulospinal-tract
- 21 - WM Right ventral-reticulospinal-tract
- 22 - WM Left ventral-corticospinal-tract
- 23 - WM Right ventral-corticospinal-tract
- 24 - WM Left tectospinal-tract
- 25 - WM Right tectospinal-tract
- 26 - WM Left medial-reticulospinal-tract
- 27 - WM Right medial-reticulospinal-tract
- 28 - WM Left medial-longitudinal-fasciculus
- 29 - WM Right medial-longitudinal-fasciculus
- 301 - GM Left medial-ventral-horn
- 302 - GM Left central-ventral-horn
- 303 - GM Left lateral-ventral-horn
- 311 - GM Right medial-ventral-horn
- 312 - GM Right central-ventral-horn
- 313 - GM Right lateral-ventral-horn
- 321 - GM Left dorsal_intermediate-zone
- 322 - GM Left ventral-intermediate-zone
- 331 - GM Right dorsal-intermediate-zone
- 332 - GM Right ventral-intermediate-zone
- 341 - GM Left reticular-formation
- 342 - GM Left dorsomarginal-nucleus
- 343 - GM Left fasciculus-dorsolateralis
- 351 - GM Right reticular-formation
- 352 - GM Right dorsomarginal-nucleus
- 353 - GM Right fasciculus-dorsolateralis
- 36 - CSF contour
- 37 - Central-canal
- 38 - Anterior-fissure
- 39 - Septum
Combined labels
- 30 - GM left ventral horn - 301:303
- 31 - GM right ventral horn - 311:313
- 32 - GM left intermediate zone - 321:322
- 33 - GM right intermediate zone - 331:332
- 34 - GM left dorsal horn - 341:343
- 35 - GM right dorsal horn - 351:353
- 50 - Spinal cord - 0:353
- 51 - White matter - 0:29
- 52 - Gray matter - 301:353
- 53 - Dorsal columns - 0:3
- 54 - Lateral funiculi - 4:13
- 55 - Ventral funiculi - 14:29
The intensities of each label in atlas/AMU7T_50_labels.nii.gz are detailed here, and the parcellation can be visualized with this Lookup table in FSLeyes and ITK-SNAP
Le Troter, A., Laines Medina, N., Mchinda, S., Cohen-Adad, J., & Callot, V. (June 2023). AMU7T : a 3D qT1 and T2*w high-resolution in vivo template with refined white and gray matter parcellation dedicated to 7T spinal cord MR analyses [Oral presentation - p. 0569]. ISMRM & ISMRT annual Meeting & Exhibition, Toronto, ON, Canada.