BRAINS Snap Shopt Writer
Description
Create 2D snap shots from multiple 3D volumes with labels. Any number of input and label could be given.
Required Input:
- at lease one inputVolumes (NO DEFAULT)
- at least inputPlaneDirection (Default is given in xml)
- inputSliceToExtract[InPercent/InIndex/InPhysicalPoint], This has to be paired to the number of inputPlaneDirection above. (default is given in xml)
Batch Processing Script
This is script to generate snap shot for auto work up.
Ex)
Bash script ex
for dir in `ls //scratch/PREDICT/B4AUTO.20120104/BAW_20120104_workflow/`
do
## t1 and t2
t1=(`ls //scratch/PREDICT/B4AUTO.20120104/BAW_20120104_workflow/$dir/11_BABC/*t1_average*`)
t2=(`ls //scratch/PREDICT/B4AUTO.20120104/BAW_20120104_workflow/$dir/11_BABC/*t2_average*`)
# structures
includeBinaries="";
for file in `ls //scratch/PREDICT/B4AUTO.20120104/BAW_20120104_workflow/$dir/_structures_*/BRAINSCUT/*_seg.nii.gz`
do
includeBinaries="$includeBinaries --inputBinaryVolumes $file"
done
inputBasename=$dir
outputDir="/scratch/PREDICT/regina/BRAINSFitCheck/B4AUTO.20120104/"
mkdir -p $outputDir
outputImage="$outputDir/${inputBasename}2DImage.png"
atlasVolume="/scratch/PREDICT/regina/BRAINS/buildICC/ReferenceAtlas-build/Atlas/Atlas_20111229/template_t1.nii.gz"
CMD="/scratch/PREDICT/regina/BRAINS/buildICC/lib/BRAINSSnapShotWriter \
--inputVolumes $t1 \
--inputVolumes $t2 \
$includeBinaries \
--inputVolumes $atlasVolume \
--inputPlaneDirection 2,1,0,0 \
--inputSliceToExtractInPhysicalPoint 0,0,10,-10 \
--outputFilename $outputImage"
echo "-------------------------------------------"
echo $CMD
if [ -s $outputImage ]; then
echo "exist"
else
script="$outputDir//Script$inputBasename.sh"
echo "$CMD" > $script
chmod 755 $script
fi
echo "-------------------------------------------"
done
Help
$ BRAINSSnapShotWriter --help
USAGE:
../../buildBRAINSCut201111215/lib/BRAINSSnapShotWriter
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--outputFilename <std::string>]
[--inputPlaneDirection
<std::vector<int>>]
[--inputSliceToExtractInPercent
<std::vector<int>>]
[--inputSliceToExtractInIndex
<std::vector<int>>]
[--inputSliceToExtractInPhysicalPoi
nt <std::vector<float>>]
[--inputBinaryVolumes
<std::vector<std::string>>] ...
[--inputVolumes
<std::vector<std::string>>] ...
[--] [--version] [-h]
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)
--xml
Produce xml description of command line arguments (default: 0)
--echo
Echo the command line arguments (default: 0)
--outputFilename <std::string>
2D file name of input images. Required.
--inputPlaneDirection <std::vector<int>>
Plane to display. In general, 0=saggital, 1=coronal, and 2=axial
plane. (default: 0,1,2)
--inputSliceToExtractInPercent <std::vector<int>>
2D slice number of input images. Percentage input from 0%-100%. (ex.
--inputSliceToExtractInPercent 50,50,50
--inputSliceToExtractInIndex <std::vector<int>>
2D slice number of input images. For size of 256*256*256 image, 128 is
usually used.
--inputSliceToExtractInPhysicalPoint <std::vector<float>>
2D slice number of input images. For autoWorkUp output, which AC-PC
aligned, 0,0,0 will be the center.
--inputBinaryVolumes <std::vector<std::string>> (accepted multiple
times)
Input mask (binary) volume list to be extracted as 2D image. Multiple
input is possible.
--inputVolumes <std::vector<std::string>> (accepted multiple times)
Input image volume list to be extracted as 2D image. Multiple input is
possible. At least one input is required.
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
Description: Create 2D snapshot of input images. Mask images are
color-coded
Author(s): Eunyoung Regina Kim
Usage
Usage A. index input by voxel index:
inputSliceToExtractInIndex Usage
BRAINSSnapShotWriter \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T1.nii.gz \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T2.nii.gz \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_SG.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_caudate.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_caudate.nii.gz \ --inputPlaneDirection 2,1,0,0 \ --inputSliceToExtractInIndex 128,128,115,135 \ --outputFilename ~/Desktop/testIndex.png
Usage B. index input by physical points:
inputSliceToExtractInPhysicalPoint
BRAINSSnapShotWriter \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T1.nii.gz \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T2.nii.gz \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_SG.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_caudate.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_caudate.nii.gz \ --inputPlaneDirection 2,1,0 \ --inputSliceToExtractInPhysicalPoint 0,0,10 \ --outputFilename ~/Desktop/testPhysicalPoints.png
Usage C. index input by percent:
inputSliceToExtractInPercent
BRAINSSnapShotWriter \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T1.nii.gz \ --inputVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/43971_AVG_T2.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_putamen.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_l_caudate.nii.gz \ --inputBinaryVolumes /paulsen/IPIG/predict_3T_MR/site-073/2334/43971/10_AUTO.NN3Tv20110418/ANN2011May04ManualCompleted/43971_r_caudate.nii.gz \ --inputPlaneDirection 2,1,0,0 \ --inputSliceToExtractInPercent 50,50,40,60 \ --outputFilename ~/Desktop/testPercents.png
