201208 - Description of Notes
This page should fill in any important notes about the project. Think of it as a page in a global lab notebook.
- Description of data to be processed
- Scripts used to process the data
- Failed processing attempts
- Successful processing attempts
New Meeting Notes Instructions -- Remove this note when finished!
- Remove this note when ready to publish
- Recommended Page Notes Name: YYYMNMDD <<Note contents>>
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- OPTIONAL Dynamic Tasklist :
{dynamictasklist:ToDo DESCRIP YYMMDD} - OPTIONAL Table of Contents: {toc:style=outline|maxLevel=2}
Data Description
Directory: /hjohnson/HDNI/ABCPaper/PreliminaryTest
Tasks attempted description
Working version ( out of BAW nipype)
bash command.sh /ipldev/scratch/eunyokim/src/BRAINS2012Jun/build/
binary=$1; $binary/lib/BRAINSABC \ --atlasDefinition $binary/ReferenceAtlas-build/Atlas/Atlas_20120627/AtlasPVDefinition.xml \ --atlasToSubjectInitialTransform /IPLlinux/hjohnson/HDNI/PREDICT_TRAINING/regina_ann/TrainingModels/BRAINSAutoWorkUpTest/B4AUTO.Regina/BAW_20120104_workflow/_uid_PHD_024_0132_38235/05_BLI/landmarkInitializer_atlas_to_subject_transform.mat \ --atlasToSubjectTransform atlas_to_subject.mat \ --debuglevel 0 \ --filterIteration 3 \ --filterMethod GradientAnisotropicDiffusion \ --gridSize 28,20,24 \ --implicitOutputs t1_average_BRAINSABC.nii.gz \ --implicitOutputs t2_average_BRAINSABC.nii.gz \ --inputVolumeTypes T1,T1,T2,T2 \ --inputVolumes /IPLlinux/hjohnson/HDNI/PREDICT_TRAINING/regina_ann/TrainingModels/BRAINSAutoWorkUpTest/B4AUTO.Regina/BAW_20120104_workflow/_uid_PHD_024_0132_38235/01_BCD/BCD_ACPC.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T1-30_3.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T2-30_4.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T2-30_5.nii.gz \ --maxBiasDegree 4 \ --maxIterations 3 \ --outputDir ./ \ --outputDirtyLabels volume_label_seg.nii.gz \ --outputFormat NIFTI \ --outputLabels brain_label_seg.nii.gz \ --outputVolumes 0132_38235_T1-30_2_corrected.nii.gz \ --outputVolumes 0132_38235_T1-30_3_corrected.nii.gz \ --outputVolumes 0132_38235_T2-30_4_corrected.nii.gz \ --outputVolumes 0132_38235_T2-30_5_corrected.nii.gz \ --posteriorTemplate POSTERIOR_%s.nii.gz \ --interpolationMode Linear
Developing version ( copy one of T2 image and see if that works: NO)
binary=$1; $binary/lib/BRAINSABC \ --atlasDefinition $binary/ReferenceAtlas-build/Atlas/Atlas_20120627/AtlasPVDefinition.xml \ --atlasToSubjectInitialTransform /IPLlinux/hjohnson/HDNI/PREDICT_TRAINING/regina_ann/TrainingModels/BRAINSAutoWorkUpTest/B4AUTO.Regina/BAW_20120104_workflow/_uid_PHD_024_0132_38235/05_BLI/landmarkInitializer_atlas_to_subject_transform.mat \ --atlasToSubjectTransform atlas_to_subject.mat \ --debuglevel 0 \ --filterIteration 3 \ --filterMethod GradientAnisotropicDiffusion \ --gridSize 28,20,24 \ --implicitOutputs t1_average_BRAINSABC.nii.gz \ --implicitOutputs t2_average_BRAINSABC.nii.gz \ --inputVolumeTypes T1,T1,T2,T2,T2 \ --inputVolumes /IPLlinux/hjohnson/HDNI/PREDICT_TRAINING/regina_ann/TrainingModels/BRAINSAutoWorkUpTest/B4AUTO.Regina/BAW_20120104_workflow/_uid_PHD_024_0132_38235/01_BCD/BCD_ACPC.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T1-30_3.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T2-30_4.nii.gz \ --inputVolumes /paulsen/MRx/PHD_024/0132/38235/ANONRAW/0132_38235_T2-30_5.nii.gz \ --inputVolumes /hjohnson/HDNI/ABCPaper/PreliminaryTest_CPT2/0132_38235_T2-30_5_copy.nii.gz \ --maxBiasDegree 4 \ --maxIterations 3 \ --outputDir ./ \ --outputDirtyLabels volume_label_seg.nii.gz \ --outputFormat NIFTI \ --outputLabels brain_label_seg.nii.gz \ --outputVolumes 0132_38235_T1-30_2_corrected.nii.gz \ --outputVolumes 0132_38235_T1-30_3_corrected.nii.gz \ --outputVolumes 0132_38235_T2-30_4_corrected.nii.gz \ --outputVolumes 0132_38235_T2-30_5_corrected.nii.gz \ --outputVolumes 0132_38235_T2-30_5_copy_corrected.nii.gz \ --posteriorTemplate POSTERIOR_%s.nii.gz \ --interpolationMode Linear
Above script will fail with following messages:
....
LowHigh Thresholds: [560,2147483647]
Correlation value between image 0 and image 1: 0.998312
Correlation value between image 0 and image 2: 0.843364
Correlation value between image 0 and image 3: 0.845546
Correlation value between image 0 and image 4: 0.845546
Correlation value between image 1 and image 2: 0.843438
Correlation value between image 1 and image 3: 0.84578
Correlation value between image 1 and image 4: 0.84578
Correlation value between image 2 and image 3: 0.995434
Correlation value between image 2 and image 4: 0.995434
Correlation value between image 3 and image 4: 1
Marking highly correlated image as duplicate :4
WARNING: Found images that were very highly correlated.
WARNING: The image /hjohnson/HDNI/ABCPaper/PreliminaryTest_CPT2/0132_38235_T2-30_5_copy.nii.gz must be removed from further processing
WARNING:
EXITING because 1 duplicates found.