Auto-generated commit for originally unversioned bundle

SCT commit: 649e113bf266182ccd3bb5e30b40c7c2393f6381 SCT commit message: BUG: updated link to binaries --> v3.0_beta16 Former-commit-id: 136ebac7aa3066f1ec26ef19013e87a162b28e5d [formerly 1a71936561feee6149b7ef87bd162bea67016860] Former-commit-id: 1acf3a1153e963939e1ed71c2cad8dae3fadc7b6 Former-commit-id: bd5c5f8291a399d2fb8e1b6077f3363199ac1c21
spinalcordtoolbox · Jul 16, 2016 · 1bd7c68 · 1bd7c68
commit 1bd7c68
Show file tree

Hide file tree

Showing 54 changed files with 145 additions and 0 deletions.
diff --git a/CHANGES.md 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
diff --git a/atlas/PAM50_atlas_01.nii.gz b/atlas/PAM50_atlas_01.nii.gz
diff --git a/atlas/PAM50_atlas_02.nii.gz b/atlas/PAM50_atlas_02.nii.gz
diff --git a/atlas/PAM50_atlas_03.nii.gz b/atlas/PAM50_atlas_03.nii.gz
diff --git a/atlas/PAM50_atlas_04.nii.gz b/atlas/PAM50_atlas_04.nii.gz
diff --git a/atlas/PAM50_atlas_05.nii.gz b/atlas/PAM50_atlas_05.nii.gz
diff --git a/atlas/PAM50_atlas_06.nii.gz b/atlas/PAM50_atlas_06.nii.gz
diff --git a/atlas/PAM50_atlas_07.nii.gz b/atlas/PAM50_atlas_07.nii.gz
diff --git a/atlas/PAM50_atlas_08.nii.gz b/atlas/PAM50_atlas_08.nii.gz
diff --git a/atlas/PAM50_atlas_09.nii.gz b/atlas/PAM50_atlas_09.nii.gz
diff --git a/atlas/PAM50_atlas_10.nii.gz b/atlas/PAM50_atlas_10.nii.gz
diff --git a/atlas/PAM50_atlas_11.nii.gz b/atlas/PAM50_atlas_11.nii.gz
diff --git a/atlas/PAM50_atlas_12.nii.gz b/atlas/PAM50_atlas_12.nii.gz
diff --git a/atlas/PAM50_atlas_13.nii.gz b/atlas/PAM50_atlas_13.nii.gz
diff --git a/atlas/PAM50_atlas_14.nii.gz b/atlas/PAM50_atlas_14.nii.gz
diff --git a/atlas/PAM50_atlas_15.nii.gz b/atlas/PAM50_atlas_15.nii.gz
diff --git a/atlas/PAM50_atlas_16.nii.gz b/atlas/PAM50_atlas_16.nii.gz
diff --git a/atlas/PAM50_atlas_17.nii.gz b/atlas/PAM50_atlas_17.nii.gz
diff --git a/atlas/PAM50_atlas_18.nii.gz b/atlas/PAM50_atlas_18.nii.gz
diff --git a/atlas/PAM50_atlas_19.nii.gz b/atlas/PAM50_atlas_19.nii.gz
diff --git a/atlas/PAM50_atlas_20.nii.gz b/atlas/PAM50_atlas_20.nii.gz
diff --git a/atlas/PAM50_atlas_21.nii.gz b/atlas/PAM50_atlas_21.nii.gz
diff --git a/atlas/PAM50_atlas_22.nii.gz b/atlas/PAM50_atlas_22.nii.gz
diff --git a/atlas/PAM50_atlas_23.nii.gz b/atlas/PAM50_atlas_23.nii.gz
diff --git a/atlas/PAM50_atlas_24.nii.gz b/atlas/PAM50_atlas_24.nii.gz
diff --git a/atlas/PAM50_atlas_25.nii.gz b/atlas/PAM50_atlas_25.nii.gz
diff --git a/atlas/PAM50_atlas_26.nii.gz b/atlas/PAM50_atlas_26.nii.gz
diff --git a/atlas/PAM50_atlas_27.nii.gz b/atlas/PAM50_atlas_27.nii.gz
diff --git a/atlas/PAM50_atlas_28.nii.gz b/atlas/PAM50_atlas_28.nii.gz
diff --git a/atlas/PAM50_atlas_29.nii.gz b/atlas/PAM50_atlas_29.nii.gz
diff --git a/atlas/PAM50_atlas_30.nii.gz b/atlas/PAM50_atlas_30.nii.gz
diff --git a/atlas/PAM50_atlas_31.nii.gz b/atlas/PAM50_atlas_31.nii.gz
diff --git a/atlas/PAM50_atlas_32.nii.gz b/atlas/PAM50_atlas_32.nii.gz
diff --git a/atlas/PAM50_atlas_33.nii.gz b/atlas/PAM50_atlas_33.nii.gz
diff --git a/atlas/PAM50_atlas_34.nii.gz b/atlas/PAM50_atlas_34.nii.gz
diff --git a/atlas/PAM50_atlas_35.nii.gz b/atlas/PAM50_atlas_35.nii.gz
diff --git a/atlas/PAM50_atlas_36.nii.gz b/atlas/PAM50_atlas_36.nii.gz
diff --git a/atlas/info_label.txt 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
diff --git a/template/PAM50_cord.nii.gz b/template/PAM50_cord.nii.gz
diff --git a/template/PAM50_csf.nii.gz b/template/PAM50_csf.nii.gz
diff --git a/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz
diff --git a/template/PAM50_label_body.nii.gz b/template/PAM50_label_body.nii.gz
diff --git a/template/PAM50_label_disc.nii.gz b/template/PAM50_label_disc.nii.gz
diff --git a/template/PAM50_label_discPosterior.nii.gz b/template/PAM50_label_discPosterior.nii.gz
diff --git a/template/PAM50_levels.nii.gz b/template/PAM50_levels.nii.gz
diff --git a/template/PAM50_levels_continuous.nii.gz b/template/PAM50_levels_continuous.nii.gz
diff --git a/template/PAM50_spine.nii.gz b/template/PAM50_spine.nii.gz
diff --git a/template/PAM50_t1.nii.gz b/template/PAM50_t1.nii.gz
diff --git a/template/PAM50_t2.nii.gz b/template/PAM50_t2.nii.gz
diff --git a/template/PAM50_t2s.nii.gz b/template/PAM50_t2s.nii.gz
diff --git a/template/PAM50_wm.nii.gz b/template/PAM50_wm.nii.gz
diff --git a/template/info_label.txt 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