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Code to process photos from UW |
FUNCTIONS / SCRIPTS (please see further info inside the individual functions / scripts) |
ReconPhotoVolume_joint_multires.m: |
Function to reconstruct a photo volume using a probabilistic atlas as reference |
ReconPhotoVolume_joint_hard_multires.m: |
Function to reconstruct a photo volume using a hard binary segmentation as reference |
makeMovieFramesHardMask.m: |
Prepares volumes and surfaces for making a registration movie using Freeview. |
Works with the output of ReconPhotoVolume_joint_hard_multires. |
It may be good in the future to write an equivalent script for ReconPhotoVolume_joint_multires.m? |
SegmentPhotosWithSAMSEG.m: |
Segments a photo reconstruction with a modified version of SAMSEG. |
SegmentMRIsWithSAMSEG.m: |
Segments an ex vivo MRIs with a modified version of SAMSEG. |
DIRECTORIES |
functions: |
A bunch of functions required by the different functions / scripts in this directory, |
including the cost functions for the optimization in ReconPhotoVolume_joint*.m |
data: |
Some SAMSEG-compatible sharedGMMparameter files, and a binarized version of the SAMSEG |
template including only the cerebrum, which is sometimes useful to initialize the segmentation |
(by registering this template with other tool or even manually, and bypassing the affine |
registration in the python SAMSEG code) |
PerspectiveNumberingBatch.*.m: different versions of software to manually annotate slices |
MakeAffineAtlases.m: makes affine atlases with / without cerebellum and brainstem |
SegmentPhotosSAMSEGscript.m: script that uses the function above to segment all cases in a directory |
SegmentMRIsWithSAMSEG.m: script to run SAMSEG on the MRIs |
CompareVolumes.m: compares volumes from MRI and photos |
%%%%%%%%%%%%%%%%%%%%%%%%% |
Old stuff... |
ReconPhotsVolume_average_onlyAtlas.m: version that uses average brain (register slices only to atlas) |
ReconPhotoVolume_average.m: version that uses average brain (registers to nrighboring slices too). |
Has a hard flag in line 178 to choose between intensities or only masks. It does something a bit crappy, |
whic is linearly registering to the average of 3 channels. Need to code this properly, and also, penalyze |
determinants so they don't go to to zero! One more thing: grouping affine transforms of slices |
within the same photo would be good! |
ReconPhotoVolume.m: prototype of code to reconstruct volume from MRI + photographs |
ReconPhotoVolume_onlyGray.m: version that uses only grayscale |
ReconPhotoVolume_binary.m: version that uses only binary mask |
ReconPhotoVolume_joint.m: uses average brain to reconstruct photos |
ReconPhotoVolume_joint_hard.m: tversion with hard labels |
ReconPhotoScript.m: uses ReconPhotoVolume_binary to reconstruct all samples in a directory |
# The format is: mergedName numberOfComponents searchStrings |
Unknown 2 Unknown Ventricle Inf-Lat-Vent Cerebellum CSF Brain-Stem Fluid_Inside_Eyes Soft_Nonbrain_Tissue Skull vessel choroid |
GlobalWM 1 Cerebral-White Optic-Chiasm |
GlobalGM 1 Cerebral-Cortex Caudate Hippocampus Amygdala hypointensities Accumbens Thalamus VentralDC Putamen Pallidum |
# The format is: mergedName numberOfComponents searchStrings |
Unknown 1 Unknown Ventricle Inf-Lat-Vent Cerebellum CSF Brain-Stem Fluid_Inside_Eyes Soft_Nonbrain_Tissue Skull vessel choroid |
GlobalWM 1 Cerebral-White Optic-Chiasm |
GlobalGM 1 Cerebral-Cortex Caudate Hippocampus Amygdala hypointensities Accumbens Thalamus VentralDC Putamen Pallidum |
# The format is: mergedName numberOfComponents searchStrings |
Unknown 2 Unknown Ventricle Inf-Lat-Vent CSF Fluid_Inside_Eyes Soft_Nonbrain_Tissue Skull vessel choroid |
GlobalWM 1 Cerebral-White Optic-Chiasm Brain-Stem Cerebellum-White |
GlobalGM 1 Cerebral-Cortex Caudate Hippocampus Amygdala hypointensities Accumbens Thalamus VentralDC Putamen Pallidum Cerebellum-Cortex |
# The format is: mergedName numberOfComponents searchStrings |
Unknown 1 Unknown Ventricle Inf-Lat-Vent Cerebellum CSF Brain-Stem Fluid_Inside_Eyes Soft_Nonbrain_Tissue Skull vessel choroid |
GlobalWM 1 Cerebral-White Optic-Chiasm |
GlobalGM 1 Cerebral-Cortex Caudate Hippocampus Amygdala hypointensities Accumbens Thalamus VentralDC Putamen Pallidum |
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