PAM50 Template

Introduction

Template-based analysis of multi-parametric MRI data of the spinal cord sets the foundation for standardization and reproducibility. Particularly, it allows researchers to process their data with minimum bias and perform multi-center studies, with the goal of improving patient diagnosis and prognosis and discovering new biomarkers of spinal-related diseases.

To perform template-based analysis, a template is needed. Templates act as a common reference space to realign each subject to. PAM50 is one such template for MRI of the full spinal cord and brainstem, and is included in your installation of SCT. “PAM” stands for “Polytechnique”, “Aix-Marseille University” and “Montreal Neurological Institute”, the three institutions that collaborated to develop the template. The PAM50 template has the following features:

• It is available for T1-, T2-and T2*-weighted MRI contrast.

• It is compatible with the ICBM152 brain template (a.k.a. the MNI coordinate system), allowing researchers to conduct simultaneous brain/spine studies within the same coordinate system.

• It includes a probabilistic atlas for white matter, gray matter, and CSF regions.

• It is a straightened template rather than a curved one.

The template is stored in the data/PAM50/ directory in your SCT installation directory. PAM50/ contains several subfolders, each corresponding to different aspects of PAM50.

Template (PAM50/template)

The template folder contains the PAM50 template for various MRI contrast types. It also contains binary and probabilistic masks for different spinal features, as well as point-wise labels for vertebral levels and intervertebral discs.

The template folder also contains an info_label.txt file to explain what each file represents:

# Template labels
# Keyword=IndivLabels (Please DO NOT change this line)
# ID, name, file
0, T1-weighted template, PAM50_t1.nii.gz
1, T2-weighted template, PAM50_t2.nii.gz
2, T2S-weighted template, PAM50_t2s.nii.gz
3, spinal cord mask (binary), PAM50_cord.nii.gz
4, white matter mask (probabilistic), PAM50_wm.nii.gz
5, gray matter mask (probabilistic), PAM50_gm.nii.gz
6, cerebrospinal fluid mask (binary), PAM50_csf.nii.gz
7, spinal cord mask with discrete vertebral levels, PAM50_levels.nii.gz
8, spinal cord mask with continuous vertebral levels, PAM50_levels_continuous.nii.gz
9, point-wise vertebral body labels, PAM50_label_body.nii.gz
10, point-wise intervertebral disc labels, PAM50_label_disc.nii.gz
11, point-wise posterior intervertebral disc labels, PAM50_label_discPosterior.nii.gz
12, spine mask (binary), PAM50_spine.nii.gz
13, spinal cord centerline, PAM50_centerline.nii.gz
14, point-wise spinal level labels, PAM50_label_spinal_levels.nii.gz

Please note that the white and gray matter masks found in template/ are for the entire structures. If you are looking for individual tracts, the relevant volumes are provided within the White and Grey Matter Atlas (PAM50/atlas) section below.

White and Grey Matter Atlas (PAM50/atlas)

The White Matter atlas will be a useful tool for your studies of specific spinal cord tracts. It consists of 36 NIfTI volumes named PAM50_atlas_<tract_number>.nii.gz where <tract_number> is the number identifying the tract. Fifteen WM tracts and three GM regions are available for each side. The values of each voxel of the files PAM50_atlas_<tract_number>.nii.gz are the voxel volume proportions occupied by the corresponding tract.

Notably, each volume is a probabilistic mask, or “soft mask”. The voxel values in these volumes range from 0 to 1; voxels in the center of each tract will equal 1, while voxels near the edges of each tract will be weighted closer to 0. This is to account for partial volume effects.

The atlas folder also contains an info_label.txt file to explain what each file represents:

# White matter atlas. Generated on: 01-Sep-2016
#
# Keyword=IndivLabels (Please DO NOT change this line)
# ID, name, file
0, WM left fasciculus gracilis, PAM50_atlas_00.nii.gz
1, WM right fasciculus gracilis, PAM50_atlas_01.nii.gz
2, WM left fasciculus cuneatus, PAM50_atlas_02.nii.gz
3, WM right fasciculus cuneatus, PAM50_atlas_03.nii.gz
4, WM left lateral corticospinal tract, PAM50_atlas_04.nii.gz
5, WM right lateral corticospinal tract, PAM50_atlas_05.nii.gz
6, WM left ventral spinocerebellar tract, PAM50_atlas_06.nii.gz
7, WM right ventral spinocerebellar tract, PAM50_atlas_07.nii.gz
8, WM left rubrospinal tract, PAM50_atlas_08.nii.gz
9, WM right rubrospinal tract, PAM50_atlas_09.nii.gz
10, WM left lateral reticulospinal tract, PAM50_atlas_10.nii.gz
11, WM right lateral reticulospinal tract, PAM50_atlas_11.nii.gz
12, WM left spinal lemniscus (spinothalamic and spinoreticular tracts), PAM50_atlas_12.nii.gz
13, WM right spinal lemniscus (spinothalamic and spinoreticular tracts), PAM50_atlas_13.nii.gz
14, WM left spino-olivary tract, PAM50_atlas_14.nii.gz
15, WM right spino-olivary tract, PAM50_atlas_15.nii.gz
16, WM left ventrolateral reticulospinal tract, PAM50_atlas_16.nii.gz
17, WM right ventrolateral reticulospinal tract, PAM50_atlas_17.nii.gz
18, WM left lateral vestibulospinal tract, PAM50_atlas_18.nii.gz
19, WM right lateral vestibulospinal tract, PAM50_atlas_19.nii.gz
20, WM left ventral reticulospinal tract, PAM50_atlas_20.nii.gz
21, WM right ventral reticulospinal tract, PAM50_atlas_21.nii.gz
22, WM left ventral corticospinal tract, PAM50_atlas_22.nii.gz
23, WM right ventral corticospinal tract, PAM50_atlas_23.nii.gz
24, WM left tectospinal tract, PAM50_atlas_24.nii.gz
25, WM right tectospinal tract, PAM50_atlas_25.nii.gz
26, WM left medial reticulospinal tract, PAM50_atlas_26.nii.gz
27, WM right medial reticulospinal tract, PAM50_atlas_27.nii.gz
28, WM left medial longitudinal fasciculus, PAM50_atlas_28.nii.gz
29, WM right medial longitudinal fasciculus, PAM50_atlas_29.nii.gz
30, GM left ventral horn, PAM50_atlas_30.nii.gz
31, GM right ventral horn, PAM50_atlas_31.nii.gz
32, GM left intermediate zone, PAM50_atlas_32.nii.gz
33, GM right intermediate zone, PAM50_atlas_33.nii.gz
34, GM left dorsal horn, PAM50_atlas_34.nii.gz
35, GM right dorsal horn, PAM50_atlas_35.nii.gz
36, CSF contour, PAM50_atlas_36.nii.gz

# Combined labels
# Keyword=CombinedLabels (Please DO NOT change this line)
# ID, name, IDgroup
50, spinal cord, 0:35
51, white matter, 0:29
52, gray matter, 30:35
53, dorsal columns, 0:3
54, lateral funiculi, 4:13
55, ventral funiculi, 14:29

# Clusters used for the first step of the MAP estimation (for advanced users only)
# Keyword=MAPLabels (Please DO NOT change this line)
# Name, IDgroup
white matter, 0:29
gray matter, 30:35
CSF, 36

Spinal levels (PAM50/spinal_levels)

In the folder data/PAM50/spinal_levels, you will find 20 label images corresponding to different spinal cord levels, spanning both C1:C8 and T1:T12. In each nifti file, the value of each voxel is the probability for this voxel to belong to the spinal level.

The spinal_levels folder also contains an info_label.txt file to explain what each file represents:

# Spinal levels labels - generated on 2016-11-28
# Keyword=IndivLabels (Please DO NOT change this line)
# ID, name, file
0, Spinal level C1, spinal_level_01.nii.gz
1, Spinal level C2, spinal_level_02.nii.gz
2, Spinal level C3, spinal_level_03.nii.gz
3, Spinal level C4, spinal_level_04.nii.gz
4, Spinal level C5, spinal_level_05.nii.gz
5, Spinal level C6, spinal_level_06.nii.gz
6, Spinal level C7, spinal_level_07.nii.gz
7, Spinal level C8, spinal_level_08.nii.gz
8, Spinal level T1, spinal_level_09.nii.gz
9, Spinal level T2, spinal_level_10.nii.gz
10, Spinal level T3, spinal_level_11.nii.gz
11, Spinal level T4, spinal_level_12.nii.gz
12, Spinal level T5, spinal_level_13.nii.gz
13, Spinal level T6, spinal_level_14.nii.gz
14, Spinal level T7, spinal_level_15.nii.gz
15, Spinal level T8, spinal_level_16.nii.gz
16, Spinal level T9, spinal_level_17.nii.gz
17, Spinal level T10, spinal_level_18.nii.gz
18, Spinal level T11, spinal_level_19.nii.gz
19, Spinal level T12, spinal_level_20.nii.gz

References

• De Leener B, Fonov VS, Collins DL, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage, 2018, 165:170-179.

• Levy S, Benhamou M, Naaman C, Rainville P, Callot V, Cohen-Adad J. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage, 2015, 119:262-271.

• Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Wilson JR, Mikulis D, Nugaeva N, Fehlings MG. Characterizing the location of spinal and vertebral levels in the human cervical spinal cord. AJNR Am J Neuroradiol, 2015, 36(4):803-810.

Additionally, the template was generated using the following tools:

• neuropoly/template GitHub repository

• White matter atlas script

• Spinal levels script