AMU7T: 3D qT1 and T2*w in vivo template + atlas

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

Data

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_atlas_ID_bin.nii.gz: Binary masks by ID.

Labels: Multilabel atlas in in atlas/AMU7T_50_labels.nii.gz containing:

ID - Region

• 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
• 5 - WM Right_lateral-corticospinal
• 6 - WM Left_ventral-spinocerebellar
• 7 - WM Right_ventral-spinocerebellar
• 8 - WM Left_rubrospinal
• 9 - WM Right_rubrospinal
• 10 - WM Left_lateral-reticulospinal
• 11 - WM Right_lateral-reticulospinal
• 12 - WM Left_spinal-lemniscus-spinothalamic
• 13 - WM Right_spinal-lemniscus-spinothalamic
• 14 - WM Left_spino-olivary
• 15 - WM Right_spino-olivary
• 16 - WM Left_ventrolateral-reticulospinal
• 17 - WM Right_ventrolateral-reticulospinal
• 18 - WM Left_lateral-vestibulospinal
• 19 - WM Right_lateral-vestibulospinal
• 20 - WM Left_ventral-reticulospinal
• 21 - WM Right_ventral-reticulospinal
• 22 - WM Left_ventral-corticospinal
• 23 - WM Right_ventral-corticospinal
• 24 - WM Left_tectospinal
• 25 - WM Right_tectospinal
• 26 - WM Left_medial-reticulospinal
• 27 - WM Right_medial-reticulospinal
• 28 - WM Left_medial-longitudinal-fasciculus
• 29 - WM Right_medial-longitudinal-fasciculus
• 30 - anterior-fissure
• 31 - septum
• 32 - GM Left_medial-ventral-horn
• 33 - GM Left_central-ventral-horn
• 34 - GM Left_lateral-ventral-horn
• 35 - GM Right_medial-ventral-horn
• 36 - GM Right_central-ventral-horn
• 37 - GM Right_lateral-ventral-horn
• 38 - GM Left_dorsal-intermediate-zone
• 39 - GM Left_ventral-intermediate-zone
• 40 - GM Right_dorsal-intermediate-zone
• 41 - GM Right_ventral-intermediate-zone
• 42 - GM Left_reticular-formation
• 43 - GM Left_dorsomarginal-nucleus
• 44 - GM Left_fasciculus-dorsolateralis
• 45 - GM Right_reticular-formation
• 46 - GM Right_dorsomarginal-nucleus
• 47 - GM Right_fasciculus-dorsolateralis
• 48 - central-canal
• 49 - CSF contour

Combined labels

• 50 - GM Left_ventral-horn, 32:34
• 51 - GM Right_ventral-horn, 35:37
• 52 - GM Left_intermediate-zone, 38:39
• 53 - GM Right_intermediate-zone, 40:41
• 54 - GM Left_dorsal-horn, 42:44
• 55 - GM Right_dorsal-horn, 45:47
• 56 - spinal-cord, 0:48
• 57 - white-matter, 0:31
• 58 - gray-matter, 32:48
• 59 - dorsal-columns, 0:3
• 60 - lateral-funiculi, 4:13
• 61 - 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

Usage: Registration of AMU7T to Subject space

For an optimal registration of the AMU7T, it is recommended to work with a WM mask that covers the dorsal horns up to the CSF (see the the animation below).

Optimal parameters for register AMU7T to subject space

sct_register_to_template -i image.nii.gz -s image_wm.nii.gz -l landmarks.nii.gz -c t1 -v 1 -s-template-id 4  -t ../template_AMU7T  -param step=1,type=imseg,algo=centermassrot,rot_method=pcahog:step=2,type=seg,algo=bsplinesyn,slicewise=0,metric=MeanSquares,samplStrategy=None,samplPercent=0.2,iter=2,smooth=1,rot_method=pcahog:step=3,type=seg,algo=syn,metric=MeanSquares,shrink=2,dof=Tz_Rz_Sz,slicewise=1,iter=20 -ref subject

Atlas registration to subject space

sct_apply_transfo -i template_AMU7T/atlas/AMU7T_50_labels.nii.gz -d image.nii.gz -w warp_template2anat.nii.gz -o labels_AMU7T2anat.nii.gz -x nn

Other uses with SCT commands

sct_warp_template -d image.nii.gz -w warp_template2anat.nii.gz  -t template_AMU7T
sct_extract_metric -i image.nii.gz -f label/atlas  -method wa -o wa_T1.csv -z 2:17 -perslice 1

Python script for registrater AMU7T template to subject space

python template_AMU7T/code/AMU7T_registration.py --path_image image.nii.gz --mask_wm image_wm.nii.gz --landmarks landmarks.nii.gz --path_template_AMU7T template_AMU7T/ --path_output OUTPUT

Related issues

#13 #4 #PR14

How to cite

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.