Merge branch 'master' of https://github.com/neuropoly/spinalcordtoolbox

# By Julien Cohen-Adad (25) and Benjamin De Leener (5)
# Via Julien Cohen-Adad (5) and Benjamin De Leener (1)
* 'master' of https://github.com/neuropoly/spinalcordtoolbox: (30 commits)
  BUG: fixed really stupid thing
  BUG: fixed supid thing
  BUG: forgot debug mode
  DOC: minor improvement
  BUG: updated new name for msct_nurbs
  DOC: updated batch_processing
  DOC: add & to fslview line for PropSeg
  DOC: CHANGES updated
  BUG: fixed bug on default values for PropSeg
  TEST: fixed wrong flag
  BIG: fixed wrong flag
  OPT: removed padding of straight landmarks before estimating pairwise transformation
  BUG: fixed input parameters
  OPT: now importing libraries inside modules
  REF: cleaning
  OPT: changed name
  DOC: display useful info in sct_crop_image. Fixed #291
  OPT: added verification if all labels provided by the user are different before registration to template. Fixed #273
  TEST: updated tests
  OPT: fixed issue #294
  ...

CHANGES.md

@@ -5,8 +5,8 @@
 
 - NEW: sct_fmri_compute_tsnr: new function to compute TSNR from fMRI data (performs moco before)
 - OPT: sct_straighten_spinalcord: now MUCH faster and more accurate (issue #240)
-- OPT: sct_register_to_template: more accurate, allows more flexibility regarding input parameters.
-       N.B. parameter "-m" has been replaced by "-s" 
+- OPT: sct_register_to_template: allows more flexibility by allowing multiple steps for registration (flag -p).
+  - N.B. flag "-m" has been replaced by "-s"
 - OPT: sct_register_multimodal: allows more flexibility by imposing only one stage. Several stages can be run sequentially and then transformations can be concatenated.
 - OPT: sct_extract_metric: new methods for extraction: maximum likelihood and maximum a posteriori, which take into account partial volume effect
 - OPT: new WM atlas: added gray matter and CSF for computing partial volume
@@ -18,6 +18,7 @@
 - OPT: straightening: improved smoothing and variable resolution
 - OPT: sct_register_multimodal: simplification of registration between multimodal images, it is now possible to use regularized slice-wise registration (SliceReg)
 - NEW: sct_get_ernst_angle: new script to compute and display Ernst angle depending on T1 and TR
+- OPT: sct_process_segmentation: now allows to compute average CSA across vertebral levels (or slices)
 
 ##1.1.2_beta (2014-12-25)
 

batch_processing.sh

@@ -16,16 +16,15 @@ cd sct_example_data
 # ===========================================================================================
 cd t2
 # spinal cord segmentation
-# tips: we use "-max-deformation 3" otherwise the segmentation does not cover the whole spinal cord
+# tips: we use "-max-deformation 4" otherwise the segmentation does not cover the whole spinal cord
 # tips: we use "-init 130" to start propagation closer to a region which would otherwise give poor segmentation (try it with and without the parameter).
-# tips: we use "-centerline-binary" to get the centerline, which can be used to initialize segmentation on other contrasts.
-sct_propseg -i t2.nii.gz -t t2 -centerline-binary -mesh -max-deformation 4 -init 130
+# tips: we use "-mesh" to get the mesh of the segmentation, which can be viewed using MITKWORKBENCH
+sct_propseg -i t2.nii.gz -t t2 -mesh -max-deformation 4 -init 130
 # check your results:
 fslview t2 -b 0,800 t2_seg -l Red -t 0.5 &
-# tips: You can also use MITKWORKBENCH to view the mesh.
 # At this point you should make labels. Here we can use the file labels.nii.gz, which contains labels at C3 (value=3) and T4 (value=11).
 # register to template
-sct_register_to_template -i t2.nii.gz -l labels.nii.gz -m t2_seg.nii.gz -o 1 -s normal -r 0
+sct_register_to_template -i t2.nii.gz -l labels.nii.gz -s t2_seg.nii.gz -r 0
 # warp template and white matter atlas
 sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz
 # compute cross-sectional area

dev/sct_crop_image/main.cpp

@@ -381,8 +381,9 @@ int transform(string inputFilename, string outputFilename, string maskFilename,
         }
 	}
 
+    cout << "Cropping the following region:" << endl;
     for (int i=0; i<N; i++)
-        cout << startSlices[i] << " " << endSlices[i] << endl;
+        cout << "Dimension " << i << ": " << startSlices[i] << " " << endSlices[i] << endl;
 
 	typename ImageType::IndexType desiredStart1;
     desiredStart1.Fill(0);

scripts/sct_nurbs.py → scripts/msct_nurbs.py

@@ -59,8 +59,6 @@
 #
 # License: see the LICENSE.TXT
 #=======================================================================================================================
-import sys
-import math
 # check if needed Python libraries are already installed or not
 try:
     from numpy import *

scripts/msct_parser.py

@@ -56,7 +56,6 @@
 #########################################################################################
 
 import sct_utils as sct
-from msct_types import *
 
 ########################################################################################################################
 ####### OPTION
@@ -263,7 +262,6 @@ def parse(self, arguments):
 
             # check if optional arguments with default values are all in the dictionary. If not, add them.
             for option in [opt for opt in self.options if not self.options[opt].mandatory]:
-                print option
                 if option not in dictionary and self.options[option].default_value:
                     dictionary[option] = self.options[option].default_value