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PAM50 Template

2024-02-15 (JV)

  • Added template/PAM50_rootlets.nii.gz. This file contains dorsal cervical (C2-C8) rootlets. The rootlets were automatically segmented using the r20240129 rootlets model (https://github.com/ivadomed/model-spinal-rootlets/releases/tag/r20240129). Then, the right side was manually adjusted (removing/adding a single voxel for some levels), and rootlets were symmetrized using code/symmetrize_cord_segmentation.py

2023-10-23 (JCA)

  • Replace individual spinal level files with a singular template/PAM50_spinal_levels.nii.gz file based on Frostell et al. paper. (#18)
  • Update the pointwise PAM50_spinal_midpoint.nii.gz file to match the new spinal levels.

2023-10-11 (JN)

  • Add cauda equinea label (60) to point label files for easier lumbar registration. (#27)

2023-09-22 (JCA)

  • Several tweaks to the PAM50 template (#21):
    • Add script that symmetrizes images.
    • Add script to update the PAM50_levels.nii.gz file using the extended cord segmentation.
    • Extend PAM50_cord.nii.gz down to L1/L2.
    • Extend rostral/caudal coverage of the PAM50_levels.nii.gz file.

2023-05-19 (JV)

  • Corrected the histology microstructure atlas (alignment with ICBM152 PAM50 space (#6), resampling to 0.2x0.2x0.5 resolution (#9))

2022-05-27 (AF)

  • Added first draft of histology microstructure atlas. (#2)

2020-11-04 (JCA)

2019-10-29 (CG)

  • Added template/PAM50_label_spinal_levels.nii.gz
  • Clarify label names in template/info_label.txt

2018-12-11 (BDL)

  • Aligned the template with the ICBM152 (more info here: spinalcordtoolbox/spinalcordtoolbox#2085)
  • Cropped the template just above C1 vertebral label
  • Updated the file info_label.txt in the folder template/ to take new files into account
  • Shifted the labels in the file PAM50_label_discPosterior.nii.gz by one

2018-08-13 (JCA)

  • Swapped ventral-dorsal labels on PAM50/atlas (fixed issue #1995)

2018-04-10 (BDL)

  • Added labels 49 (pontomedullary groove) and 50 (pontomedullary junction) to template/PAM50_label_disc.nii.gz

2017-01-07 (JCA)

  • Fixed typo in atlas info_label.txt (issue #1100)

2017-01-01 (JCA)

  • Atlas now sums to one inside the cord (fixed issue #411)

2016-11-28 (JCA)

  • added spinal levels using $SCT_DIR/dev/spinal_level/sct_extract_spinal_levels.py
  • Removed __MACOSX in archive and zip using
zip -r 20161121_PAM50.zip PAM50/

2016-11-21 (JCA)

  • Added #Keyword= entries for cleaner code

2016-07-15 (JCA)

  • Modified cord segmentation because slightly too large.
  • Symmetrized cord segmentation
  • Updated CSF + levels
  • Improved AMU->PAM50 registration
  • Regenerated PAM50_atlas based on new registration
  • Regenerated PAM50_cord, PAM50_wm and PAM50_gm as a sum of all tracts
sct_propseg -i PAM50_t1.nii.gz -c t1
# manual edits
# symmetrized cord then binarized
sct_maths -i PAM50_cord2.nii.gz -symmetrize 0 -o PAM50_cord2_sym.nii.gz
sct_maths -i PAM50_cord2_sym.nii.gz -bin -o PAM50_cord2_sym_bin.nii.gz
# add old cord to csf
sct_maths -i PAM50_cord.nii.gz -add PAM50_csf.nii.gz -o PAM50_cordcsf.nii.gz
# then substract with new cord segmentation
sct_maths -i PAM50_cordcsf.nii.gz -sub PAM50_cord2_sym_bin.nii.gz -o PAM50_csf2.nii.gz
# update levels
sct_maths -i PAM50_cord2_sym_bin.nii.gz -mul PAM50_levels.nii.gz -o PAM50_levels2.nii.gz
# register AMU->PAM50
sct_maths -i PAM50_cord.nii.gz -laplacian 1 -o PAM50_cord_lapl.nii.gz
sct_maths -i PAM50_wm.nii.gz -add PAM50_gm.nii.gz -o PAM50_wmgm.nii.gz
sct_maths -i PAM50_wmgm.nii.gz -thr 0.5 -o PAM50_wmgm_thr.nii.gz
sct_maths -i PAM50_wmgm_thr.nii.gz -bin -o PAM50_wmgm_thr_bin.nii.gz
sct_maths -i PAM50_wmgm_thr_bin.nii.gz -laplacian 1 -o PAM50_wmgm_thr_bin_lapl.nii.gz
sct_register_multimodal -i PAM50_wmgm_thr_bin_lapl.nii.gz -d PAM50_cord_lapl.nii.gz -iseg PAM50_wmgm_thr_bin.nii.gz -dseg PAM50_cord.nii.gz -param step=1,type=seg,algo=slicereg,smooth=3:step=2,type=im,algo=bsplinesyn,iter=5,slicewise=0 -x linear
sct_apply_transfo -i PAM50_wm.nii.gz -d PAM50_cord.nii.gz -w warp_PAM50_wmgm_thr_bin_lapl2PAM50_cord_lapl.nii.gz -x linear

2016-07-11 (JCA)

  • fixed issue in info_label.txt

2016-07-11 (JCA)

  • added WM atlas + GM parcellation.

2016-07-10 (JCA)

  • added info_label.txt

2016-07-10 (JCA)

  • WM/GM->float32, T2s->uint16, WM/GM/T2s->RPI

2016-07-10 (BDL)

  • Added WM, GM and T2s

2016-07-05 (CG)

  • Added PAM50_spine.nii.gz

2016-07-01 (JCA):

  • Reduced size of C1 vertebrae.

2016-07-01 (JCA)

  • Fixed wrong z-values in PAM50_label_disc.

2016-07-01 (JCA)

  • Changed PAM50_label* to type=uint8 because values were non-integer.

2016-06-29 (JCA)

  • Changed orientation for RPI
  • fixed inconsistent sizes
  • thresholded at zero
  • set type=uint16 for t1,t2 and t2s
  • added continuous vertebral levels.
old_file=PAM50_WM
new_file="/Users/julien/Dropbox/Public/sct/PAM50/template/PAM50_wm"
sct_maths -i ${old_file}.nii.gz -thr 0 -o tmp.file.nii.gz
sct_image -i tmp.file.nii.gz -type float32 -o tmp.file.nii.gz
sct_image -i tmp.file.nii.gz -setorient RPI -o tmp.file.nii.gz
mv tmp.file.nii.gz ${new_file}.nii.gz

2016-06-21 (BDL)

  • Modified T1-T2 coregistration
  • updated T2*

2016-03-26 (JCA)

2015-11-04 (BDL)

  • Creation