BRAINS
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  • 201208 Starter: BRAINSABC trials
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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.

  1. Description of data to be processed
  2. Scripts used to process the data
  3. Failed processing attempts
  4. Successful processing attempts

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Data Description

Directory:  /hjohnson/HDNI/ABCPaper/PreliminaryTest

Tasks attempted description

Working version ( out of BAW nipype)

Running on terminal

bash command.sh /ipldev/scratch/eunyokim/src/BRAINS2012Jun/build/

Working version test: /hjohnson/HDNI/ABCPaper/PreliminaryTest/PreliminaryTest/command.sh
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)

Developing version : /hjohnson/HDNI/ABCPaper/PreliminaryTest_CPT2/command.sh
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.

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