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

Main Dependencies

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.
• template/AMU7T_levels.nii.gz: SC mask with discrete vertebral levels.
• 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.

Multilabel atlas containing:

atlas/

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

ID	Region
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

Note :

• List of clases on atlas/AMU7T_50_labels.nii.gz is detailed here,
• For a good visualization of parcellations use these LookUp Tables : FSLeyes, ITK-SNAP

Usage:

1. Automatic segmentations and vertebral labeling using sct_deepseg

SC segmentation: spinalcord model

sct_deepseg spinalcord -install

sct_deepseg spinalcord -i IMAGE.nii.gz  -o IMAGE_sc_seg.nii.gz

GM segmentation: graymatter model

sct_deepseg graymatter -install

sct_deepseg graymatter -i IMAGE.nii.gz  -o IMAGE_gm_seg.nii.gz 

WM segmentation:

sct_maths -i IMAGE_sc_seg.nii.gz -sub IMAGE_gm_seg.nii.gz  -o IMAGE_wm_seg.nii.gz

⚠️ Warning: Manually correct WM segmentation if necessary.

Vertebral labeling: totalspineseg model

sct_deepseg totalspineseg -install

sct_deepseg totalspineseg -i IMAGE.nii.gz  -step 1 -o  IMAGE_total.nii.gz

2. AMU7T Registration

2.1 Registration of Template to Subject space

sct_register_to_template
        -i IMAGE.nii.gz
        -s IMAGE_wm_seg.nii.gz
        -ldisc IMAGE_total_step_1_levels.nii.gz
        -t $template_AMU7T_path
        -c t1
        -s-template-id 4
        -ref subject 
        -param step=0,type=label,algo=syn,rot_method=pca,dof=Tx_Ty_Tz_Rz:
              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=3,smooth=1,rot_method=pca:
              step=3,type=seg,algo=syn,metric=MeanSquares,shrink=2,dof=Tz_Rz_Sz,slicewise=1,iter=20
        -ofolder AMU7T_2_IMAGE

2.2. Registration of Atlas

Warp template and all atlases to Subject space

sct_warp_template
        -d IMAGE.nii.gz
        -w AMU7T_2_IMAGE/warp_template2anat.nii.gz
        -t $template_AMU7T_path
        -ofolder AMU7T_2_IMAGE

Warp multilabel atlas

sct_apply_transfo
        -i $template_AMU7T_path/atlas/AMU7T_50_labels.nii.gz
        -d IMAGE.nii.gz
        -w AMU7T_2_IMAGE/warp_template2anat.nii.gz
        -x nn
        -o AMU7T_2_IMAGE/AMU7T_50_labels_2_IMAGE.nii.gz

2.3 Extract quantitative metrics

sct_extract_metric
        -i IMAGE.nii.gz
        -f AMU7T_2_IMAGE/label/atlas
        -method wa
        -z 2:17
        -perslice 1
        -o AMU7T_2_IMAGE/IMAGE_wa_T1.csv

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.