updated batch_processing and CHANGES

CHANGES.md

@@ -1,6 +1,7 @@
 # CHANGES TO RELEASE
 
 ##3.0 (TBD)
+- NEW: PAM50 template now used as the default template
 - NEW: **sct_compute_snr**: compute SNR using several methods (Dietrich et al. 2007)
 - NEW: **sct_propseg**: now accepts a correction solution for sct_propseg in case of missing CSF/SC contrast and/or artefacts (see issue #664 for details)
 - NEW: **sct_propseg**: added flag to open a viewer for initializing spinal cord segmentation by manually providing a few points (issue #741)
@@ -9,13 +10,16 @@
 - NEW: **sct_dmri_create_noisemask**: Identification and estimation of noise in the diffusion signal, implemented by the Dipy software project (http://nipy.org/dipy/), based on the PIESNO method
 - NEW: **sct_register_graymatter**: Multi-label registration that accounts for gray matter shape.
 - NEW: **sct_register_multimodal**: features two new transformations: centermassrot and columnwise.
+- BUG: **sct_straighten_spinalcord**: Fixed #917, #924
 - BUG: Fixed issues #715, #719
 - BUG: **sct_propseg**: fixed issues #147, #242, #309, #376, #501, #544, #674, #680
 - BUG: **sct_segment_graymatter**: fixed issues #782, #813, #815
-- BUG: fixed incompatibility with CENTOS 6.X (issue #776)
+- BUG: Fixed incompatibility with CENTOS 6.X (issue #776)
+- BUG: Binaries now hosted on Gihub for accessibility from China (#927)
 - OPT: **sct_check_dependencies**: Made test more sentitive to OS incompatibilities (issue #771)
 - OPT: **sct_register_multimodal**: major changes. Simplified flags. Fixed issues #350, #404, #414, #499, #650, #735, #737, #749, #807, #818
 - OPT: **sct_register_to_template**: now uses slicewise rigid transfo at first step (instead of slicereg), which improves accuracy (issue #666)
+- OPT: **sct_label_vertebrae**: now fully automatic (although unstable-- work in progress).
 
 ##2.2.3 (2016-02-04)
 - BUG: **sct_straighten_spinalcord**: fixed instabilities related to generation of labels (issue #722)

batch_processing.sh

@@ -39,54 +39,46 @@ if [ $DISPLAY = true ]; then
   fslview t2 -b 0,800 t2_seg -l Red -t 0.5 &
 fi
 # Vertebral labeling. Here we use the fact that the FOV is centered at C7.
-sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -initcenter 7
+sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -initcenter 7
 # Create labels at C3 and T2 vertebral levels
-sct_label_utils -i t2_seg_labeled.nii.gz -label-vert 3,9
+sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 3,9
 # Register to template
-sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels.nii.gz
+sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels.nii.gz -c t2
 # Warp template without the white matter atlas (we don't need it at this point)
 sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0
 # check results
 if [ $DISPLAY = true ]; then
-  fslview t2.nii.gz -b 0,800 label/template/MNI-Poly-AMU_T2.nii.gz -b 0,4000 label/template/MNI-Poly-AMU_level.nii.gz -l MGH-Cortical -t 0.5 label/template/MNI-Poly-AMU_GM.nii.gz -l Red-Yellow -b 0.5,1 label/template/MNI-Poly-AMU_WM.nii.gz -l Blue-Lightblue -b 0.5,1 &
+  fslview t2.nii.gz -b 0,800 label/template/PAM50_t2.nii.gz -b 0,4000 label/template/PAM50_levels.nii.gz -l MGH-Cortical -t 0.5 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.5,1 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.5,1 &
 fi
 # compute average cross-sectional area and volume between C3 and C4 levels
 sct_process_segmentation -i t2_seg.nii.gz -p csa -vert 3:4
 # go back to root folder
 cd ..
 
-
-#  t1
-# ----------
+# t1
+# ===========================================================================================
 cd t1
-# spinal cord segmentation
+# Spinal cord segmentation
 sct_propseg -i t1.nii.gz -c t1
-# check results
+# Check results:
 if [ $DISPLAY = true ]; then
-  fslview t1 -b 0,800 t1_seg -l Red -t 0.5 &
+  fslview t1 -b 0,800 t2_seg -l Red -t 0.5 &
 fi
-# create mask around spinal cord (for cropping)
-sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 61 -f box -o mask_t1.nii.gz
-# crop t1 and t1_seg (for faster registration)
-sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz -o t1_crop.nii.gz
-sct_crop_image -i t1_seg.nii.gz -m mask_t1.nii.gz -o t1_seg_crop.nii.gz
-# register to template (which was previously registered to the t2).
-sct_register_multimodal -i ../t2/label/template/MNI-Poly-AMU_T2.nii.gz -iseg ../t2/label/template/MNI-Poly-AMU_cord.nii.gz -d t1_crop.nii.gz -dseg t1_seg_crop.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=im,algo=syn,iter=3,gradStep=0.2,metric=CC
-# concatenate transformations
-sct_concat_transfo -w ../t2/warp_template2anat.nii.gz,warp_MNI-Poly-AMU_T22t1_crop.nii.gz -d t1.nii.gz -o warp_template2t1.nii.gz
-sct_concat_transfo -w warp_t1_crop2MNI-Poly-AMU_T2.nii.gz,../t2/warp_anat2template.nii.gz -d $SCT_DIR/data/template/MNI-Poly-AMU_T2.nii.gz -o warp_t12template.nii.gz
+# Vertebral labeling. Here we use the fact that the FOV is centered at C7.
+sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -initcenter 7
+# Create labels at C3 and T2 vertebral levels
+sct_label_utils -i t2_seg_labeled.nii.gz -label-vert 3,9
+# Register to template
+sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels.nii.gz
 # Warp template without the white matter atlas (we don't need it at this point)
-sct_warp_template -d t1.nii.gz -w warp_template2t1.nii.gz -a 0
-# Check results
-if [ $DISPLAY = true ]; then
-  fslview t1.nii.gz label/template/MNI-Poly-AMU_T2.nii.gz -b 0,4000 label/template/MNI-Poly-AMU_level.nii.gz -l MGH-Cortical -t 0.5 label/template/MNI-Poly-AMU_GM.nii.gz -l Red-Yellow -b 0.5,1 label/template/MNI-Poly-AMU_WM.nii.gz -l Blue-Lightblue -b 0.5,1 &
-fi
-# warp T1 to template space
-sct_apply_transfo -i t1.nii.gz -d $SCT_DIR/data/template/MNI-Poly-AMU_T2.nii.gz -w warp_t12template.nii.gz
-# check registration of T1 to template
+sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0
+# check results
 if [ $DISPLAY = true ]; then
-  fslview $SCT_DIR/data/template/MNI-Poly-AMU_T2.nii.gz -b 0,4000 t1_reg.nii.gz -b 0,800 &
+  fslview t2.nii.gz -b 0,800 label/template/PAM50_t2.nii.gz -b 0,4000 label/template/PAM50_levels.nii.gz -l MGH-Cortical -t 0.5 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.5,1 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.5,1 &
 fi
+# compute average cross-sectional area and volume between C3 and C4 levels
+sct_process_segmentation -i t2_seg.nii.gz -p csa -vert 3:4
+# go back to root folder
 cd ..
 
 

commit.txt

@@ -1 +1 @@
-2e97bf0ee479c726bc3acca2d79b187c3cece9c4
+0a8be8eab4c8a29fda28a65c2f80910f0e7612ce