PAM50 Template

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/pam50/pam50_template.png

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, perform multi-center studies, with the goal of improving patient diagnosis and prognosis and helping the discovery of new biomarkers of spinal-related diseases.

PAM50 is one such template for MRI of the full spinal cord and brainstem, and is included in your installation of SCT. It 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. MNI template), allowing to conduct simultaneous brain/spine studies within the same coordinate system.

  • It includes atlases of white matter pathways and gray matter subregions.

Template (PAM50/template)

The template folder contains image files representing different template diffusion weightings, binary/probablistic masks (for the spinal cord, WM/GM tracts, etc.), and 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

White and grey matter atlas (PAM50/atlas)

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/pam50/white_matter_atlas_illustration.png

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.

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)

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/pam50/spinal_levels_illustration.png

In the folder data/PAM50/spinal_levels, you will find 20 label images corresponding to different spinal cord levels, including 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