| Code to process photos from UW |
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| FUNCTIONS / SCRIPTS (please see further info inside the individual functions / scripts) |
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| ReconPhotoVolume_joint_multires.m: |
| Function to reconstruct a photo volume using a probabilistic atlas as reference |
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| ReconPhotoVolume_joint_hard_multires.m: |
| Function to reconstruct a photo volume using a hard binary segmentation as reference |
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| 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? |
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| SegmentPhotosWithSAMSEG.m: |
| Segments a photo reconstruction with a modified version of SAMSEG. |
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| SegmentMRIsWithSAMSEG.m: |
| Segments an ex vivo MRIs with a modified version of SAMSEG. |
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| DIRECTORIES |
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| 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 |
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| 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) |
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| PerspectiveNumberingBatch.*.m: different versions of software to manually annotate slices |
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| MakeAffineAtlases.m: makes affine atlases with / without cerebellum and brainstem |
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| SegmentPhotosSAMSEGscript.m: script that uses the function above to segment all cases in a directory |
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| SegmentMRIsWithSAMSEG.m: script to run SAMSEG on the MRIs |
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| CompareVolumes.m: compares volumes from MRI and photos |
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| %%%%%%%%%%%%%%%%%%%%%%%%% |
| Old stuff... |
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| 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! |
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| ReconPhotoVolume.m: prototype of code to reconstruct volume from MRI + photographs |
| ReconPhotoVolume_onlyGray.m: version that uses only grayscale |
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| ReconPhotoVolume_binary.m: version that uses only binary mask |
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| ReconPhotoVolume_joint.m: uses average brain to reconstruct photos |
| ReconPhotoVolume_joint_hard.m: tversion with hard labels |
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| ReconPhotoScript.m: uses ReconPhotoVolume_binary to reconstruct all samples in a directory |
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