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Medlea activity tracker


Activity recorder
Date
Activity Name
Activity Duration (Approx Hrs)
Category
Comments
20 March 2025
AI learning
0
7
​
19 March 2025
Learning AI
0
2
Started learning bits of AI
19 March 2025
Studying papers on AI usage for spirometry
0
5
Studied papers on AI usage for spirometry, seems recent studies have been able to do it
18 March 2025
Analysis of lobe ratio with FEV
0
7
Did analysis of lobe volume ratio to preop FEV for Gemelli patients
17 March 2025
Paper study on empirical FEV
0
5
Studied an interesting paper about empirical postop FEV from preop FEV
17 March 2025
Weresp demo meeting
0
2
Weresp demo meeting with Satish
14 March 2025
More tests with water as fluid
0
3
Tested for higher pressure difference by simulating with water. Same problem of error in BC
14 March 2025
Literature search for empirical models of spirometry prediction
0
4
Found a paper where the POST op FEV is predicted as an empirical value of Lung expansion and other parameters. Had an idea to create something similar, where FVC predicted as function of lobe size and flow ratio
13 March 2025
Proper sized geometry test for BC
0
5
Simulation and analysis of proper sized geometry.There is definitely some bug in the BC condition, have to check for larger pressure difference
13 March 2025
Meeting with Simone
0
2
Demonstrate to SImone about bug in BC in Moebius
12 March 2025
Documenting issue with pressure pressure BC
0
7
Tried to document the issue of pressure pressure BC both on a sample geometry and on the airway T1- T3 cases
11 March 2025
Issue in pressure output in Meobius
0
7
Tried to find out the cause for pressure error. Moebius outputs an unphyiscal pressure at the end cells, which messes up the average. So now use the centerline pressure
10 March 2025
Simulation for T2
0
7
Had huge problem in creating geometries for T2. Satisfied all conditions of watertightness, but due to a small fragment, it was giving problem in meshing. Finally was able to get the meshing done
7 March 2025
Meeting with Simone
0
1
Meeting with Simone. Discussed about approach of Spanish group. Decided to use the inlet velocity as a calibration to get the pressure and then use it to get FEV etc.
7 March 2025
Analysis of pressure vs flow simulation
0
2
Modified some points in the report as there was a bug in the scripts.
7 March 2025
Airway segmentation using MONAI module
0
5
Segmentation of 60 cases (30 PRE and 30 POST) using Monai auto segmentation. 2. Creating side by side comparison images of STLs and producing a doc file
6 March 2025
Simulating effects of grid, pressure difference
0
4
Setting up simulations for T1 POST, handled the CFL error by reducing Mach number 2. Setting up pressure BC simulations for measuring flow rate at trachea
6 March 2025
Analysis of POST results and pressure variation
0
3
Spent creating scripts to analyse the flow distribution for POST 2. Analysis of flow measurement for different pressures 3. Tried a lot of ways to create consistent linking between ipynb files and .py files, but could not do it after lot of attempts
5 March 2025
Creating and modifying analysis scripts
0
4
Improved and corrected errors in the analysis scripts for analysing the flow rates, pressure and other parameters
5 March 2025
Comparison of previous and new model
0
3
Created a report comparing the airflow distribution between previous airway+parenchymna model and current only airway model. Airway distribution shows signifcant changes from the normal CT volumetric based prediction
4 March 2025
Framework for analyis fluxes from the simulations
0
4
1. Spent lot of time writing scripts. 2. Main issues in postprocessing - inlet/outlet faces are not aligned with axes, have to determine the proper normals and centroid from the VTP, then a cut plane a few mesh points inside the domain by moving along the surface normal. 2. Had to clip data in a spherical region and then take slice, otherwise extra regions get included in the slice
4 March 2025
Simulations for airway model
0
3
1. Simulated T1 PRE and POST after modifying the STLs. 2. Crashing due to CFL happening, had to test many parameters and finally settled on Mach 0.01 with constant inflow BC
3 March 2025
Setting up framework for creating simulations
0
7
1. Created the entire framework for converting from Slicer STL to final VTP. 2. Got stuck with problem in cleaning mesh after exporting from Blender and later creating the FaceID from that. Now process will be a) Export STL from Slicer. b)Clean and watertight (script created) c) Tag in Blender and export obj 4) Create FaceID from Blender OBJ and export final VTP
28 February 2025
Reading PhD thesis on spirometry simulation
0
2
PhD thesis of Fernandez compiles the papers on the lung spirometry simulation. Although the approach seemed a bit odd, have to think more about it!
28 February 2025
Creating VTPs for simulation wiith Blender
0
5
The remote machine is not working, so not able to run simulations. 2. Creating VTPs for T1 POST and T2 _PRE and POST in Blender. 3. Creating the python scripts for automating some of the tasks of the VTP creation, like scaling and creation of FaceID scalar.
27 February 2025
Setting up simulation for new model
0
7
The
run.py
⁠
was executing the meshing step at each run, so was wasting lot of time. Created the code to enable/disable discretization as per need. 2. Tried to resolve the CFL crashing by softening the sudden spike of pressure due to BC. Created a ramp function and a step function for pressure. 3. Seems there is bug in time loop with BCs, gives some error after some time (not a CFL error).
26 February 2025
Meeting with Simone
0
1
Meeting to discuss about CFL crashing in pressure - pressure BC
26 February 2025
Using Blender for VTP creation for simulation
0
4
Created the framework for tagging faces with Blender, then exporting to VTP for final configuration. Also created scripts to check watertight STLs, scaling operations and final FaceID scalar creation as per Moebius rule
26 February 2025
Exploring Blender as an alternative for STL face tagging
0
3
Blender learning continued, steep learning curve, but very powerful and flexible
25 February 2025
Exploring Blender as an alternative for STL face tagging
0
2
Learnt the basics of Blender from Youtube tutorials and materials, seemed most efficient in terms of STL face selection
25 February 2025
Meeting
0
1
Meeting with Simone to discuss and setup Gmoebius on my system
25 February 2025
Creating simulation setup from STL
0
4
Explored Gmoebius and tried to create the VTP for simulation. Lot of problems faced - 1. The selected traingles for tagging donot appear correctly (I think it is a display issue!) 2. Sometimes the substract mesh operation was not working properly. Overall, realised neither Meshlab nor Gmoebius will be good candidate for creating VTPs from STL, as the most critical and difficult part was the tagging of faces and both of them had below par selection interface. So need to find a software where STL manipulation/selection is most convenient.
24 February 2025
Install gmoebius
0
4
Trying to install gmoebius. Facing lots of problem - 1. Had to experiment with various ways to have another python 3.10.12 installed without affecting the default python 2. pip install from file was skipping packages, so had to use another command - cat pip-requirements | xargs -n 1 pip install. Still couldnot figure out, will need to take help of Simone tomorrow
24 February 2025
Setup of airway simulation with pressure BCs
0
3
Trying to discretize the vtp directly from a
run.py
⁠
code, also setting up gmoebius on my system for easy creation of files. First simulation with pressure pressure BCs on a truncated geometry sucessful. Mesh generated from the vtp through code, not through Gmoebius. Imp point that I realised after some trials - VTP has to be scaled by 0.001 to ensure proper units.
21 February 2025
STL modification for inlet outlet modification
0
7
Spent time and figured out the complete steps to truncate STL, close holes, paint inlets/outlets. Finally export the STL with ‘color’ functions defined which can be used in Paraview to define FaceID scalar (necessary for Moebius meshing)
20 February 2025
Airway segmentation for Gemelli POST
0
6
T26 took a lot of time to remove kinks on the lobe surfaces. Completed segmentation for T26 to T29. Spent lot of time on T30, but could not do it, as CT quality seemed to be poor, as well as orientation was tilted.
20 February 2025
STL modification for inlet outlet modification
0
1
Explored different ways to label outlets from the airway STL. Thinking of Meshlab as an option, will have to study more. Maybe start with a truncated airway with only two bronchus ans see if it can tagged and readied for simulation.
19 February 2025
Airway segmentation for Gemelli POST
0
7
Segmented PRE cases from T21 to T25. Needed time to run Lungmask on my system for all the cases (does not have GPU and no GUI access to remote machine for Slicer access on it) and then modify segmentations. Specially, case T23 and T25 took lot of time to remove kinks on the lobes surface.
18 February 2025
Papers on spirometry through CFD
0
3
Collected multile cited papers and also PhD thesis of Fernandez, created summary in Onenote about spirometry, model and applied BCs.
18 February 2025
Airway segmentation for Gemelli POST
0
4
Segmented cases from T26 to T29, had to redo T21 due to error. Tried T30, but lobe demarcation couldnot be identified, so failed to do it!
17 February 2025
Group meeting with John (Demcon) and clinicians from Leiden
0
4
Detailed meeting on ventilators and possibilty of prediction of ventilator performance through CFD simulations. Lot of focus on tissue effects due to flow and also appopriate ways to model patient degeneration etc.
17 February 2025
New model for lungs
0
3
Collected multiple papers on airflow and CFD simulation
There are no rows in this table
170
Sum
⁠
Weekly time distribution
⁠

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