20130125 - Experiments-Compare Affine and Syn
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
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Related JIRA ticket
Data Description
- Working Dir: /IPLlinux/hjohnson/HDNI/20130225_BRAINSABC_Publication/BRAINSABC_Affine
- Roughly pick two sessions per site regarding variety of ventricle sizes: We are regarding ventricle size as a indicative of brain shrinkage. Dave is working on providing measures of CSF, (WM+GM)/CSF to see if those are better for indicative. I will pick data set baseed on those.
BSD (Brain Simulated Data from Montreal Group) Test
Directory:
/IPLlinux/hjohnson/HDNI/20130125_BRAINSABC_Publication/BRAINSABC_brainweb/SegmentationComparison/CompareToGroundTruth
Python Script to Compute Similarities:
R Script for Plot
Plot: Well at lease onething worked..
Dice Index | Hausdorff Distance Average |
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Tasks attempted description
Check if BRAINSABC works with Affine only registration.
Working Dir: /IPLlinux/hjohnson/HDNI/20130225_BRAINSABC_Publication/BRAINSABC_Affine
inputDir="/IPLlinux/hjohnson/HDNI/20130225_BRAINSABC_Publication/BRAINSABC_Affine" BRAINSABC \ --atlasDefinition $inputDir/ExtendedAtlasDefinition.xml \ --atlasToSubjectInitialTransform $inputDir/landmarkInitializer_atlas_to_subject_transform.h5 \ --atlasToSubjectTransform atlas_to_subject.h5 \ --atlasToSubjectTransformType Affine \ --debuglevel 10 \ --filterIteration 3 \ --filterMethod GradientAnisotropicDiffusion \ --gridSize 10,10,10 \ --inputVolumeTypes T1,T1,T2 \ --inputVolumes $inputDir/subject_t1_01.nii.gz \ --inputVolumes $inputDir/subject_t1_02.nii.gz \ --inputVolumes $inputDir/subject_t2_01.nii.gz \ --interpolationMode Linear \ --maxBiasDegree 4 \ --maxIterations 3 \ --outputDir ./ \ --outputDirtyLabels volume_label_seg.nii.gz \ --outputFormat NIFTI \ --outputLabels brain_label_seg.nii.gz \ --outputVolumes subject_T1-30_2_corrected.nii.gz \ --outputVolumes subject_T1-30_3_corrected.nii.gz \ --outputVolumes subject_T2-30_4_corrected.nii.gz \ --posteriorTemplate POSTERIOR_%s.nii.gz