ENH: cleaner example

README.md

@@ -5,10 +5,15 @@ A simple and "fast" brain registration example
 
 We use a brain mask to restrict the registration focus
 
-Similar strategies may be used for brains with missing data e.g. lesions 
+Similar strategies may be used for brains with missing data e.g. lesions
 
 Both cases are illustrated in this [example script](https://github.com/stnava/BasicBrainMapping/blob/master/bbm.sh).
 
+From within the directory, do:
+
+```sh
+ bash bbm.sh data/IXI/T_template2.nii.gz data/IXI594-Guys-1089-T1.nii.gz data/neg_lesion.nii.gz 
+```
 
 ![T1_lesioned](https://raw.github.com/stnava/BasicBrainMapping/master/T1_lesioned.jpg?raw=true)
 ![Template2T1_lesioned](https://raw.github.com/stnava/BasicBrainMapping/master/Template2T1_lesioned.jpg?raw=true)

bbm.sh

@@ -3,68 +3,12 @@ dim=3 # image dimensionality
 AP="" # /home/yourself/code/ANTS/bin/bin/  # path to ANTs binaries
 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4  # controls multi-threading
 export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
-f=$1 ; m=$2 ; mask=$3   # fixed and moving image file names
-if [[ ${#f} -eq 0 ]] ; then 
-echo usage is 
-echo $0 fixed.nii.gz moving.nii.gz  fixed_brain_mask.nii.gz 
-exit
-fi
-if [[ ! -s $f ]] ; then echo no fixed $f ; exit; fi
-if [[ ! -s $mask ]] ; then echo no fixed mask $mask ; exit; fi
-if [[ ! -s $m ]] ; then echo no moving $m ;exit; fi
-reg=${AP}antsRegistration           # path to antsRegistration
-its=10000x1111x5
-percentage=0.25
-syn="20x20x0,0,5"
-nm=BBM
-imgs=" $f, $m "
-if [[ ! -s  ${nm}0GenericAffine.mat ]] ; then 
-$reg -d $dim -r [ $imgs ,1]  \
-                        -m mattes[  $imgs , 1 , 32, regular, 0.05 ] \
-                         -t translation[ 0.1 ] \
-                         -c [1000,1.e-8,20]  \
-                        -s 4vox  \
-                        -f 6 -l 1 \
-                        -m mattes[  $imgs , 1 , 32, regular, 0.1 ] \
-                         -t rigid[ 0.1 ] \
-                         -c [1000x1000,1.e-8,20]  \
-                        -s 4x2vox  \
-                        -f 4x2 -l 1 \
-                        -m mattes[  $imgs , 1 , 32, regular, 0.1 ] \
-                         -t affine[ 0.1 ] \
-                         -c [$its,1.e-8,20]  \
-                        -s 4x2x1vox  \
-                        -f 3x2x1 -l 1 \
-                        -m mattes[  $imgs , 1 , 32 ] \
-                         -t SyN[ .20, 3, 0 ] \
-                         -c [ $syn ]  \
-                        -s 1x0.5x0vox  \
-                        -f 4x2x1 -l 1 -u 1 -z 1 -x $mask --float 1 \
-                       -o [${nm},${nm}_diff.nii.gz,${nm}_inv.nii.gz]
-${AP}antsApplyTransforms -d $dim -i $m -r $f -n linear -t ${nm}1Warp.nii.gz -t ${nm}0GenericAffine.mat -o ${nm}_warped.nii.gz --float 1 
-fi  
-
-echo Lesion study uses the affine mapping from the previous result.
-echo One could also "revise" the template mask by the lesion mask but 
-echo here we assume the affine map is not corrupted by the lesion. 
-echo We do, however, mask the deformation estimation with a lesion mask.
-origmat=${nm}0GenericAffine.mat
 nm=BBM_Lesion
-SmoothImage 3 data/lesion.nii.gz 2 data/neg_lesion.nii.gz
-ImageMath 3  data/neg_lesion.nii.gz CorruptImage  data/neg_lesion.nii.gz 
-ImageMath 3 data/neg_lesion.nii.gz Neg data/neg_lesion.nii.gz 
-MultiplyImages 3 data/neg_lesion.nii.gz $2 data/T1_lesioned.nii.gz 
-m=data/T1_lesioned.nii.gz
-imgs=" $m, $f "
-myit=1000
-$reg -d $dim -r [${origmat},1] \
-    -m mattes[  $imgs , 1 , 32 ] \
-    -t SyN[ .20, 3, 0.1 ] \
-    -c [ 30x20x0 ]  \
-    -s 1x0.5x0vox  \
-    -f 4x2x1 -l 1 -u 1 -z 1 -x data/neg_lesion.nii.gz   \
-    -o [${nm},${nm}_diff.nii.gz,${nm}_inv.nii.gz]
-ExtractSliceFromImage 3 data/T1_lesioned.nii.gz temp.nii.gz 1 120
-ConvertImagePixelType temp.nii.gz T1_lesioned.jpg 1
-ExtractSliceFromImage 3 ${nm}_diff.nii.gz temp.nii.gz 1 120
-ConvertImagePixelType temp.nii.gz Template2T1_lesioned.jpg 1
+echo Users should consider doing affine registration without the mask
+echo and deformable registration with the mask
+MultiplyImages 3 data/IXI594-Guys-1089-T1.nii.gz data/neg_lesion.nii.gz  data/T1_lesioned.nii.gz
+antsRegistrationSyNQuick.sh -d 3 -f data/IXI/T_template2.nii.gz \
+  -m data/T1_lesioned.nii.gz -t s -o ${nm}_diff -x data/neg_lesion.nii.gz
+rm grid.nii.gz jacobian.nii.gz
+CreateJacobianDeterminantImage 3 ${nm}_diff1Warp.nii.gz jacobian.nii.gz 1
+CreateWarpedGridImage 3 ${nm}_diff1Warp.nii.gz grid.nii.gz 1x0x1 10x10x10 3x3x3