Analysis: Write script for generating presegmentations for FALCON validation

[LalithShiyam]

Clinicians will find it remarkably hard to segment all the major regions in PET. Would make sense if we could do some presegmentations using MOOSE models.

[LalithShiyam]

Update 1: Presegmentations of the CT are done for all the Siemens healthy volunteers.

Remaining task: Need to register the CT (moving) to the PET frames (fixed) individually and transfer the presegmentations to the PET, for the clinicians to rectify. Boy this is gonna take long.

[LalithShiyam]

Update 2: Presegmentations of the CT needs to be cleared of trachea. Will definitely need @josefyu's efforts.

[josefyu]

so the last status was, morph CT to make it visible with PET, since the PET are the dynamic images and CT is only avaible for 1 timepoint. Please let me know, when we can look together on the CT presegmentations (file location).

[LalithShiyam]

@josefyu Basically it's what I had mentioned in update: 2, we have the datasets (CT + CT segmentation), we need to clean up the trachea before I warp the CTs to different PET frames (along with their segmentations). So the to-do list is the following:

• [x] @LalithShiyam creates a standardised folder structure optimised for the subsequent process

• [x] @josefyu: clears the trachea from the dataset, uploaded to MOOSE computer, I would be needing the names as usual (segment names renamed)

• [ ] @LalithShiyam: will convert the corrected nrrd to nifti with the correct segmentation.

• [x] @LalithShiyam: will create a script to align the CT and its segmentation with the dynamic PET.

• [ ] @josefyu: will check if the aligned segmentations are accurate (different task).

[LalithShiyam]

Folder structure implemented:

.
├── Sub001
│   ├── AC_LOWD_CT_WB_4_0_2_0_HD_FOV
│   ├── nifti
│   │   ├── CT           # CT image in nifti
│   │   ├── label        # Actual label in nifti after @josefyu correction
│   │   ├── label-NRRD   # Actual label in nrrd after @josefyu correction    
│   │   ├── paired-CT    # Multiple CT frames now in alignment with 3d PT 
│   │   ├── paired-label # Multiple label frames now in alignment with 3d PT
│   │   ├── paired-PT    # Individual 3d PT frames  
│   │   └── PT           # 4d PT frame
│   └── PET_WB_DYNAMIC_(QC)_0006
│       └── nifti
│           └── split3d
│               └── moco
├── Sub002
│   ├── AC_LOWD_CT_WB_4_0_2_0_HD_FOV
│   ├── nifti
│   │   ├── CT
│   │   ├── label
│   │   ├── label-NRRD
│   │   ├── paired-CT
│   │   ├── paired-label
│   │   ├── paired-PT
│   │   └── PT
│   └── PET_WB_DYNAMIC_(QC)_0006
│       └── nifti
│           └── split3d
│               └── moco

[LalithShiyam]

Script workflow align_ct_with_3dpet.py

• [x] Split 4d PT nifti file into 3d PT nifti files
• [x] Align (affine) the single CT file (moving) with each of the 3d PT files (fixed)
• [x] Use the transform files to apply them to the rectified label.

[josefyu]

@josefyu Basically it's what I had mentioned in update: 2, we have the datasets (CT + CT segmentation), we need to clean up the trachea before I warp the CTs to different PET frames (along with their segmentations). So the to-do list is the following:

• [x] @LalithShiyam creates a standardised folder structure optimised for the subsequent process
• [x] @josefyu: clears the trachea from the dataset, uploaded to MOOSE PC, I would be needing the names as usual (segment names renamed)
• [ ] @LalithShiyam: will convert the corrected nrrd to nifti with the correct segmentation.
• [x] @LalithShiyam: will create a script to align the CT and its segmentation with the dynamic PET.
• [ ] @josefyu: will check if the aligned segmentations are accurate (different task).

https://filesender.aco.net/?s=download&token=ece76841-f41b-42b0-a533-5cb5627a0b76

Labels cleared from trachea, saved as .nrrd, segments renamed as anatomical namings. note: some of the liver/kidneys segmentations are bad, tried to correct all errors.

[LalithShiyam]

Awesome, thank you @josefyu! The segmentations and the CT's are being aligned with the dynamic PET frames. We should have the results in a couple of hours! So I am closing this issue!