diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 0000000..a2b3aa7 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,86 @@ +#PAM50 Template + +##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) +- Fixed https://github.com/neuropoly/spinalcordtoolbox/issues/783 + +##2015-11-04 (BDL) +- Creation + +##TODO: +- also adjust size of PAM50_levels_continuous.nii.gz +- 2016-07-15: PAM50_levels is missing some voxels compared to PAM50_cord (due to adjustmen) diff --git a/atlas/PAM50_atlas_00.nii.gz b/atlas/PAM50_atlas_00.nii.gz new file mode 100644 index 0000000..f2e739e Binary files /dev/null and b/atlas/PAM50_atlas_00.nii.gz differ diff --git a/atlas/PAM50_atlas_01.nii.gz b/atlas/PAM50_atlas_01.nii.gz new file mode 100644 index 0000000..c89bbe0 Binary files /dev/null and b/atlas/PAM50_atlas_01.nii.gz differ diff --git a/atlas/PAM50_atlas_02.nii.gz b/atlas/PAM50_atlas_02.nii.gz new file mode 100644 index 0000000..ca82217 Binary files /dev/null and b/atlas/PAM50_atlas_02.nii.gz differ diff --git a/atlas/PAM50_atlas_03.nii.gz b/atlas/PAM50_atlas_03.nii.gz new file mode 100644 index 0000000..738b730 Binary files /dev/null and b/atlas/PAM50_atlas_03.nii.gz differ diff --git a/atlas/PAM50_atlas_04.nii.gz b/atlas/PAM50_atlas_04.nii.gz new file mode 100644 index 0000000..4e6e42d Binary files /dev/null and b/atlas/PAM50_atlas_04.nii.gz differ diff --git a/atlas/PAM50_atlas_05.nii.gz b/atlas/PAM50_atlas_05.nii.gz new file mode 100644 index 0000000..fc1d478 Binary files /dev/null and b/atlas/PAM50_atlas_05.nii.gz differ diff --git a/atlas/PAM50_atlas_06.nii.gz b/atlas/PAM50_atlas_06.nii.gz new file mode 100644 index 0000000..0694313 Binary files /dev/null and b/atlas/PAM50_atlas_06.nii.gz differ diff --git a/atlas/PAM50_atlas_07.nii.gz b/atlas/PAM50_atlas_07.nii.gz new file mode 100644 index 0000000..b923be8 Binary files /dev/null and b/atlas/PAM50_atlas_07.nii.gz differ diff --git a/atlas/PAM50_atlas_08.nii.gz b/atlas/PAM50_atlas_08.nii.gz new file mode 100644 index 0000000..536d99a Binary files /dev/null and b/atlas/PAM50_atlas_08.nii.gz differ diff --git a/atlas/PAM50_atlas_09.nii.gz b/atlas/PAM50_atlas_09.nii.gz new file mode 100644 index 0000000..655a761 Binary files /dev/null and b/atlas/PAM50_atlas_09.nii.gz differ diff --git a/atlas/PAM50_atlas_10.nii.gz b/atlas/PAM50_atlas_10.nii.gz new file mode 100644 index 0000000..169cef9 Binary files /dev/null and b/atlas/PAM50_atlas_10.nii.gz differ diff --git a/atlas/PAM50_atlas_11.nii.gz b/atlas/PAM50_atlas_11.nii.gz new file mode 100644 index 0000000..fa15dae Binary files /dev/null and b/atlas/PAM50_atlas_11.nii.gz differ diff --git a/atlas/PAM50_atlas_12.nii.gz b/atlas/PAM50_atlas_12.nii.gz new file mode 100644 index 0000000..439d577 Binary files /dev/null and b/atlas/PAM50_atlas_12.nii.gz differ diff --git a/atlas/PAM50_atlas_13.nii.gz b/atlas/PAM50_atlas_13.nii.gz new file mode 100644 index 0000000..816e79e Binary files /dev/null and b/atlas/PAM50_atlas_13.nii.gz differ diff --git a/atlas/PAM50_atlas_14.nii.gz b/atlas/PAM50_atlas_14.nii.gz new file mode 100644 index 0000000..c5cd934 Binary files /dev/null and b/atlas/PAM50_atlas_14.nii.gz differ diff --git a/atlas/PAM50_atlas_15.nii.gz b/atlas/PAM50_atlas_15.nii.gz new file mode 100644 index 0000000..4b15ac5 Binary files /dev/null and b/atlas/PAM50_atlas_15.nii.gz differ diff --git a/atlas/PAM50_atlas_16.nii.gz b/atlas/PAM50_atlas_16.nii.gz new file mode 100644 index 0000000..ff347ce Binary files /dev/null and b/atlas/PAM50_atlas_16.nii.gz differ diff --git a/atlas/PAM50_atlas_17.nii.gz b/atlas/PAM50_atlas_17.nii.gz new file mode 100644 index 0000000..59f7375 Binary files /dev/null and b/atlas/PAM50_atlas_17.nii.gz differ diff --git a/atlas/PAM50_atlas_18.nii.gz b/atlas/PAM50_atlas_18.nii.gz new file mode 100644 index 0000000..203a862 Binary files /dev/null and b/atlas/PAM50_atlas_18.nii.gz differ diff --git a/atlas/PAM50_atlas_19.nii.gz b/atlas/PAM50_atlas_19.nii.gz new file mode 100644 index 0000000..d0e3777 Binary files /dev/null and b/atlas/PAM50_atlas_19.nii.gz differ diff --git a/atlas/PAM50_atlas_20.nii.gz b/atlas/PAM50_atlas_20.nii.gz new file mode 100644 index 0000000..d6042ce Binary files /dev/null and b/atlas/PAM50_atlas_20.nii.gz differ diff --git a/atlas/PAM50_atlas_21.nii.gz b/atlas/PAM50_atlas_21.nii.gz new file mode 100644 index 0000000..9116478 Binary files /dev/null and b/atlas/PAM50_atlas_21.nii.gz differ diff --git a/atlas/PAM50_atlas_22.nii.gz b/atlas/PAM50_atlas_22.nii.gz new file mode 100644 index 0000000..0fe0961 Binary files /dev/null and b/atlas/PAM50_atlas_22.nii.gz differ diff --git a/atlas/PAM50_atlas_23.nii.gz b/atlas/PAM50_atlas_23.nii.gz new file mode 100644 index 0000000..9ee3ecb Binary files /dev/null and b/atlas/PAM50_atlas_23.nii.gz differ diff --git a/atlas/PAM50_atlas_24.nii.gz b/atlas/PAM50_atlas_24.nii.gz new file mode 100644 index 0000000..3ce478c Binary files /dev/null and b/atlas/PAM50_atlas_24.nii.gz differ diff --git a/atlas/PAM50_atlas_25.nii.gz b/atlas/PAM50_atlas_25.nii.gz new file mode 100644 index 0000000..eaeacc5 Binary files /dev/null and b/atlas/PAM50_atlas_25.nii.gz differ diff --git a/atlas/PAM50_atlas_26.nii.gz b/atlas/PAM50_atlas_26.nii.gz new file mode 100644 index 0000000..657a88e Binary files /dev/null and b/atlas/PAM50_atlas_26.nii.gz differ diff --git a/atlas/PAM50_atlas_27.nii.gz b/atlas/PAM50_atlas_27.nii.gz new file mode 100644 index 0000000..0ee6ac9 Binary files /dev/null and b/atlas/PAM50_atlas_27.nii.gz differ diff --git a/atlas/PAM50_atlas_28.nii.gz b/atlas/PAM50_atlas_28.nii.gz new file mode 100644 index 0000000..b9d296d Binary files /dev/null and b/atlas/PAM50_atlas_28.nii.gz differ diff --git a/atlas/PAM50_atlas_29.nii.gz b/atlas/PAM50_atlas_29.nii.gz new file mode 100644 index 0000000..9e78afa Binary files /dev/null and b/atlas/PAM50_atlas_29.nii.gz differ diff --git a/atlas/PAM50_atlas_30.nii.gz b/atlas/PAM50_atlas_30.nii.gz new file mode 100644 index 0000000..cae61b6 Binary files /dev/null and b/atlas/PAM50_atlas_30.nii.gz differ diff --git a/atlas/PAM50_atlas_31.nii.gz b/atlas/PAM50_atlas_31.nii.gz new file mode 100644 index 0000000..92739da Binary files /dev/null and b/atlas/PAM50_atlas_31.nii.gz differ diff --git a/atlas/PAM50_atlas_32.nii.gz b/atlas/PAM50_atlas_32.nii.gz new file mode 100644 index 0000000..769d85f Binary files /dev/null and b/atlas/PAM50_atlas_32.nii.gz differ diff --git a/atlas/PAM50_atlas_33.nii.gz b/atlas/PAM50_atlas_33.nii.gz new file mode 100644 index 0000000..2987250 Binary files /dev/null and b/atlas/PAM50_atlas_33.nii.gz differ diff --git a/atlas/PAM50_atlas_34.nii.gz b/atlas/PAM50_atlas_34.nii.gz new file mode 100644 index 0000000..9f92e0d Binary files /dev/null and b/atlas/PAM50_atlas_34.nii.gz differ diff --git a/atlas/PAM50_atlas_35.nii.gz b/atlas/PAM50_atlas_35.nii.gz new file mode 100644 index 0000000..1d45bfc Binary files /dev/null and b/atlas/PAM50_atlas_35.nii.gz differ diff --git a/atlas/PAM50_atlas_36.nii.gz b/atlas/PAM50_atlas_36.nii.gz new file mode 100644 index 0000000..c8cd404 Binary files /dev/null and b/atlas/PAM50_atlas_36.nii.gz differ diff --git a/atlas/info_label.txt b/atlas/info_label.txt new file mode 100644 index 0000000..835c9da --- /dev/null +++ b/atlas/info_label.txt @@ -0,0 +1,48 @@ +# White matter atlas. Generated on: 16-Jul-2016 +# 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 dorsal horn, PAM50_atlas_30.nii.gz +31, GM right dorsal 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 ventral horn, PAM50_atlas_34.nii.gz +35, GM right ventral horn, PAM50_atlas_35.nii.gz +36, CSF contour, PAM50_atlas_36.nii.gz + +# Combined labels +# ID, name, file +50, spinal cord, 0:35 +51, white matter, 0:29 +52, gray matter, 30:35 +52, dorsal columns, 0:3 +53, lateral funiculi, 4:13 +54, ventral funiculi, 14:29 diff --git a/template/PAM50_centerline.nii.gz b/template/PAM50_centerline.nii.gz new file mode 100644 index 0000000..8623ee6 Binary files /dev/null and b/template/PAM50_centerline.nii.gz differ diff --git a/template/PAM50_cord.nii.gz b/template/PAM50_cord.nii.gz new file mode 100644 index 0000000..8f054a8 Binary files /dev/null and b/template/PAM50_cord.nii.gz differ diff --git a/template/PAM50_csf.nii.gz b/template/PAM50_csf.nii.gz new file mode 100644 index 0000000..81c972d Binary files /dev/null and b/template/PAM50_csf.nii.gz differ diff --git a/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz new file mode 100644 index 0000000..4ce1bc6 Binary files /dev/null and b/template/PAM50_gm.nii.gz differ diff --git a/template/PAM50_label_body.nii.gz b/template/PAM50_label_body.nii.gz new file mode 100644 index 0000000..aa85789 Binary files /dev/null and b/template/PAM50_label_body.nii.gz differ diff --git a/template/PAM50_label_disc.nii.gz b/template/PAM50_label_disc.nii.gz new file mode 100644 index 0000000..4a0d07d Binary files /dev/null and b/template/PAM50_label_disc.nii.gz differ diff --git a/template/PAM50_label_discPosterior.nii.gz b/template/PAM50_label_discPosterior.nii.gz new file mode 100644 index 0000000..2f6f89e Binary files /dev/null and b/template/PAM50_label_discPosterior.nii.gz differ diff --git a/template/PAM50_levels.nii.gz b/template/PAM50_levels.nii.gz new file mode 100644 index 0000000..2bbf8ef Binary files /dev/null and b/template/PAM50_levels.nii.gz differ diff --git a/template/PAM50_levels_continuous.nii.gz b/template/PAM50_levels_continuous.nii.gz new file mode 100644 index 0000000..451c14c Binary files /dev/null and b/template/PAM50_levels_continuous.nii.gz differ diff --git a/template/PAM50_spine.nii.gz b/template/PAM50_spine.nii.gz new file mode 100644 index 0000000..e95500d Binary files /dev/null and b/template/PAM50_spine.nii.gz differ diff --git a/template/PAM50_t1.nii.gz b/template/PAM50_t1.nii.gz new file mode 100644 index 0000000..31a5d8e Binary files /dev/null and b/template/PAM50_t1.nii.gz differ diff --git a/template/PAM50_t2.nii.gz b/template/PAM50_t2.nii.gz new file mode 100644 index 0000000..207ffb9 Binary files /dev/null and b/template/PAM50_t2.nii.gz differ diff --git a/template/PAM50_t2s.nii.gz b/template/PAM50_t2s.nii.gz new file mode 100644 index 0000000..0a3f57e Binary files /dev/null and b/template/PAM50_t2s.nii.gz differ diff --git a/template/PAM50_wm.nii.gz b/template/PAM50_wm.nii.gz new file mode 100644 index 0000000..721a351 Binary files /dev/null and b/template/PAM50_wm.nii.gz differ diff --git a/template/info_label.txt b/template/info_label.txt new file mode 100644 index 0000000..96c3442 --- /dev/null +++ b/template/info_label.txt @@ -0,0 +1,11 @@ +# Template labels +# PLEASE DO NOT EDIT THE 2nd FIELD! (name) +# ID, name, file +0, T1-weighted template, PAM50_t1.nii.gz +1, T2-weighted template, PAM50_t2.nii.gz +2, T2*-weighted template, PAM50_t2s.nii.gz +3, spinal cord, PAM50_cord.nii.gz +4, white matter, PAM50_wm.nii.gz +5, gray matter, PAM50_gm.nii.gz +6, cerebrospinal fluid, PAM50_csf.nii.gz +7, vertebral labeling, PAM50_levels.nii.gz