versionhistory.txt

<b>Version history</b>
V 1.0
Initial version

V 1.1

right and left lung mask drop down segment selectors added
processing routine checks existence and name of 'Right lung mask' and 'Left lung mask'
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V 2.0 

code made efficient and modular - thanks Andras Lasso (PERK)
real-time volume rendering
immediate updated of the color categorization, both in 2D and 3D (using colormaps and volume rendering)
better GUI

V 2.1 

New extension "Lung CT Segmenter" created from https://github.com/rbumm/SlicerLungMaskGenerator
Improvements of lung segmenter module by Andras Lasso (PERK)

V 2.2 

Show / hide 2D segments automatically
implemented warning dialog before enabling 3D display 

V 2.32 

version
PDF changes

V 2.34 

Segmenter: Resampled volume levels are now adjusted to what users select for their input volume (identical brightness and contrast after 'Start')  

V 2.35 

Implementation of CSV export in CT Lung Analyzer logic - can be (and has been) called via script
Analyzer: CSV export button - will produce a file in the report directory

V 2.36 

'Autoshrink masks (1 mm)' added in Lung CT Segmenter. Produces 'cleaner' lung masks which cover less pleura, pericardium and diaphragma. 
Analyzer: CSV export button - will produce a csv file in the report directory

V 2.37 

"Regional analysis" checkbox and function added in Lung CT Analyzer. Creates ventral, dorsal, upper, middle and lower result segmentations.   
"COVID-result table" reordered and renamed to "Extended results table"
COVID-Q renamed to AF-Q (for more general use)
CSV export now exports two result tables directly 

V 2.38 

A/F-Q finally removed from the extended results table after realizing its non-linear character. The usage of the linear "% affected" parameter is recommended instead.  
"Segment Editor Extra Effects" check:  Bug removed.
"Infitrated" and "Collapsed" (ml and %) added to the extended results table.

V 2.39
Bug in the extended results table removed
"Check for updates" state now saved in configparser

V 2.40 

remove small island function disabled in Lung CT Analyzer (unpredictable results) 
emphysema color changed from black to green for a better display

V 2.41

- right and left lung masks are set visible as they should before "Segment statistics" for centroids
- setDefaultThresholds() function implemented for use via scripts
- ability to include or exclude emphysematic bullae from "affected" calculation in the extended results table  

V 2.42

- lung vessels are now solidified, reducing collapse error
- thresholds are now saved globally and locally (in the directory of the CT volume). "Load thresholds" prefers to load the local threshold dict, if not found, loads global dict
- we now have a progress bar.
- there is an option to shrink lung masks by 1 mm if Lung CT Analyzer ist used via script 

V 2.44

- LungCTSegmenter automatically generates a labelmap from it's segmentation output that is compatible with "Parenchyma analysis" of the CIP

V 2.44

- Airway segmentation (CIP) implemented 

V 2.45

- do not remember 

V 2.46

- Checks inputFilename in saveFiducialsGloballyAndLocally to avoid exception 

V 2.47

Segmenter: CIP airway segmentation removed, 'Local threshold' airway segmentation included.  

V 2.48

Implement AirwayThresholdRangeWidget and use airway thesholds in 'Local threshold' airway segmentation method.  
Improve post-segmentation workflow in LungCTSegmenter UI - enable 'Cancel/Reset', disable 'Start'

V 2.49
enhance markup re-usability in LungCTSegmenter workflow

- always save a copy of segmenter markups in Slicer temp directory for later use when pressing "Apply"
- add new checkbox "load last saved markups" effective when pressing "Start" 
- do not store segmenter data in Slicer root
- improve tooltexts
Make 2D and 3D visibility failsafe (always on) after 'Apply'  
- remove 'l' hotkey from Lung CT Segmenter for loading markups

V 2.50 
save ini settings in slicer.app.slicerUserSettingsFilePath/LCTA.ini

V 2.51 
add SNOMED International tags or lungs and trachea, set "Smoothing factor","0.2" not to suppress airway details

V 2.52
add experimental AI segmentation: lungmask U-net lung and lobe segmentation

V 2.53
add experimental AI segmentation: TotalSegmentator nn-Unet lung, lobe, airway and vessel segmentation
make the experimental engine selectable 

V 2.54
maintanace

V 2.55
Switch back to fourupview when cancel/reset is pressed
Automatically set lung CT window/level preset when Segmenter is initialized

V 2.56
Support Micro-CT (rodents)  

V 2.57
Segmenter: 
AI: support all lungmask AI models
AI: support inference from MONAILabel lung_segmentation server
start processing immediately if AI checked only and start button pressed

V 2.58
implement segmentation of thorac cavity
optional vesselmask segmentation (checkbox) 
vessel threshold slider

V 2.59
add volume rendering button 

V 2.60
add TotalSegmentator options: --fast --statistics --radiomics
change TotalSegmentator lobe colors
smooth TotalSegmentator lobes and lungs

V 2.61
make LCTA compatible with 3D SLicer 5.2.1
add SlicerTotalSegmentator support

V 2.62
Lung CT Analyzer: add lobe analysis

V 2.64

ENH: add optional NIFTI input and output in Lung CT Segmenter batch processing 

V 2.65

ENH: implement CT data calibration 
 
V 2.66

ENH: Implement Lung CT Analyzer NIFTI input and output 

V 2.67

MAINT: Change infer mode of lungmask AI which was established in a lungmask version change (2.0.14)

V 2.68

ENH: Add upper half and lower half of the lungs in both segmenter and analyzer. 
BUG: Remove header bug in regionresults.csv

V 2.69

BUG: Remove bug calculating functional volume in extended (infiltration) analysis

2024-10-04 Repository moved to https://github.com/Slicer/SlicerLungCTAnalyzer