JoHof/lungmask issues and pull requests

#112 - Inferencing Using Lungmask

Issue - State: open - Opened by abhishekpatil32 11 days ago - 2 comments

#107 - URLError when using LTRCLobes_R231 and LTRCLobes models on GPU

Issue - State: open - Opened by karolinasenkow 8 months ago - 1 comment

#106 - Dev

Pull Request - State: closed - Opened by JoHof 11 months ago

#105 - Update cli

Pull Request - State: closed - Opened by JoHof 11 months ago

#104 - Keep Patient / Study data of the input.

Pull Request - State: closed - Opened by sogorla1 11 months ago - 1 comment

#103 - Add device as a parameter to indicate in which gpu to run

Issue - State: open - Opened by xrafael 12 months ago - 1 comment

#102 - Which version of SimpleITK should be used？

Issue - State: closed - Opened by yixuanli1230 about 1 year ago - 2 comments
Labels: question

#98 - Segmentation names

Issue - State: closed - Opened by Renal-Of-Loon about 1 year ago - 1 comment

#97 - Failed to compute results: module ‘torch.backends’ has no attribute ‘mps’ ERROR

Issue - State: closed - Opened by JohanDiazTovar about 1 year ago - 1 comment

#95 - Check for Apple Metal support and use if available

Pull Request - State: closed - Opened by Andrew0Hill over 1 year ago
Labels: enhancement

#94 - Can I extract the exterior polygons of the thorax and the polygons of lungs?

Issue - State: closed - Opened by liubenyuan over 1 year ago - 1 comment
Labels: question

#93 - Remove dependency versions

Pull Request - State: closed - Opened by JoHof over 1 year ago

#92 - SimpleITK

Issue - State: closed - Opened by rbumm over 1 year ago - 6 comments

#91 - Bump pillow from 9.5.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#90 - Bump urllib3 from 1.26.15 to 1.26.17

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#89 - LTRC link in README is outdated/dead

Issue - State: closed - Opened by Renal-Of-Loon over 1 year ago - 1 comment

#88 - Bump certifi from 2022.12.7 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#87 - Improve speed

Pull Request - State: closed - Opened by rapotekhin over 1 year ago

#86 - package logger and no logging propagation

Pull Request - State: closed - Opened by JoHof over 1 year ago

#85 - how to quit lungmask environment after using

Issue - State: closed - Opened by Sere1nz over 1 year ago - 1 comment

#84 - Bump scipy from 1.9.1 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#83 - Fix/no download when path

Pull Request - State: closed - Opened by JoHof over 1 year ago

#82 - `LMInferer` should be instantiated with a model (or model path) as a parameter

Issue - State: closed - Opened by gacou54 over 1 year ago - 3 comments
Labels: bug

#81 - Request for Possibility to Adapt Lungmask from 2D U-Net to 3D U-Net

Issue - State: open - Opened by catkatze over 1 year ago

#80 - how to fine tune

Issue - State: closed - Opened by MOMOANNIE over 1 year ago - 1 comment

#79 - Bump requests from 2.28.2 to 2.31.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#78 - Code cleaning

Pull Request - State: closed - Opened by JoHof almost 2 years ago

#77 - Improved code readability and optimized for speed

Pull Request - State: closed - Opened by ajinkya-kulkarni almost 2 years ago - 1 comment

#76 - Bump torch from 1.2.0 to 1.13.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#75 - Fix/postprocessing

Pull Request - State: closed - Opened by JoHof about 2 years ago

#74 - fix spare compare way in util.py

Pull Request - State: closed - Opened by JoHof about 2 years ago

#73 - fix spare compare way in util.py

Pull Request - State: closed - Opened by zenshay about 2 years ago - 1 comment

#72 - blank in the file name seems not work.

Issue - State: closed - Opened by zh-zhang1984 about 2 years ago

#71 - :bug: changing deprecated numpy alias to standard python builtin type

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#70 - numpy 1.24 compatibility

Issue - State: closed - Opened by rbturnbull about 2 years ago
Labels: bug

#69 - How to fine-tune the lobe model

Issue - State: closed - Opened by MOMOANNIE about 2 years ago

#68 - Bump numpy from 1.17.2 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#67 - Publish package

Issue - State: closed - Opened by andreasala98 over 2 years ago - 4 comments

#66 - Add option for verbosity

Issue - State: closed - Opened by andreasala98 over 2 years ago - 1 comment

#65 - Possible Performance Improvement for Postrocessing

Issue - State: closed - Opened by william-silversmith almost 3 years ago - 4 comments

#64 - Link to LTRC dataset

Issue - State: closed - Opened by coderAddy almost 3 years ago

#63 - model returns zeros as segmentation

Issue - State: closed - Opened by epb378 almost 3 years ago - 7 comments

#62 - Error reading .dcm files

Issue - State: closed - Opened by isglobal-brge about 3 years ago - 5 comments

#61 - Meaning of values returned by mask.apply(input_image) using U-net(R231) model?

Issue - State: closed - Opened by AlphonsG about 3 years ago - 2 comments

#60 - SError: [Errno 24] Too many open files when applying lung mask on many DICOM images in a directory

Issue - State: closed - Opened by ethanmoyer over 3 years ago - 5 comments

#59 - Remove num_workers option from validation DataLoader

Pull Request - State: closed - Opened by amakropoulos over 3 years ago

#58 - understanding coding from Johannes Hofmanninger

Pull Request - State: closed - Opened by christiansucavelando over 3 years ago

#57 - Segmentation on LIDC-IDRI Dataset

Issue - State: closed - Opened by devaletanmay over 3 years ago - 4 comments

#56 - Is there a way to silence the progress bars?

Issue - State: closed - Opened by mattwarkentin over 3 years ago

#55 - Master2 creational pattern

Pull Request - State: closed - Opened by jialongshi1994 over 3 years ago

#54 - Master1 for structural pattern

Pull Request - State: closed - Opened by jialongshi1994 over 3 years ago

#53 - Model class

Pull Request - State: closed - Opened by tp61 over 3 years ago

#52 - Mask class

Pull Request - State: closed - Opened by tp61 over 3 years ago

#51 - add second pull( new class named MaskHandler ) for lab8 by jialongshi

Pull Request - State: closed - Opened by jialongshi1994 over 3 years ago

#50 - add first pull( new class named ImageDataHandler ) for lab8 by jialongshi

Pull Request - State: closed - Opened by jialongshi1994 over 3 years ago - 1 comment

#49 - Lab8 2

Pull Request - State: closed - Opened by david19990531 over 3 years ago

#48 - Lab8 1

Pull Request - State: closed - Opened by david19990531 over 3 years ago

#47 - Daemonic processes are not allowed to have children

Issue - State: closed - Opened by pesfahanian over 3 years ago

#46 - Support image as numpy array

Pull Request - State: closed - Opened by masadcv over 3 years ago - 1 comment

#45 - Question about direction pre-processing one liner

Issue - State: closed - Opened by dscarmo almost 4 years ago - 2 comments
Labels: question

#44 - ValueError: numpy.ndarray size changed, may indicate binary incompatibility

Issue - State: closed - Opened by manjitullal almost 4 years ago - 2 comments

#43 - Error when processing directory to directory

Issue - State: closed - Opened by davidssmith almost 4 years ago - 3 comments

#42 - Loss functions

Issue - State: closed - Opened by PeterMcGor about 4 years ago - 4 comments

#41 - Getting the error

Issue - State: closed - Opened by sushantag9 about 4 years ago

#40 - Apply mask on png image

Issue - State: closed - Opened by IsabelleCur about 4 years ago - 4 comments

#39 - TIF Files

Issue - State: closed - Opened by saranggoel about 4 years ago - 16 comments

#38 - Question about broken pipe error

Issue - State: closed - Opened by hrktkhs about 4 years ago - 4 comments

#37 - Finetune or re-train

Issue - State: closed - Opened by AkhilaPerumalla123 about 4 years ago

#36 - so i am using a .nii file, and its giving me all black images. I have tried using the '--nopostprocess' flag and then not using it, but nothing changed. My .nii file has multiple slices.

Issue - State: closed - Opened by saranggoel about 4 years ago - 1 comment

#35 - Dataset availability

Issue - State: closed - Opened by FabianIsensee over 4 years ago - 7 comments

#34 - Pre-trained models

Issue - State: closed - Opened by dipayandas97 over 4 years ago - 3 comments

#33 - How to get a segmented image?

Issue - State: closed - Opened by MadisLemsalu over 4 years ago - 1 comment

#32 - Fix encoding for long_description in setup.py

Pull Request - State: closed - Opened by hnguyentt over 4 years ago - 1 comment

#31 - png dataset failed.

Issue - State: closed - Opened by chuxiang93 over 4 years ago

#30 - question about dataset acquisition.

Issue - State: closed - Opened by chuxiang93 over 4 years ago

#29 - My own nii file failed, it seems that the error is caused by the zooming in and out of the image?

Issue - State: closed - Opened by chuxiang93 over 4 years ago - 3 comments

#28 - Recursive lungmask?

Issue - State: closed - Opened by MadisLemsalu over 4 years ago - 1 comment

#27 - how to get the LTRCLobes_R231 model

Issue - State: closed - Opened by ziqiangxu almost 5 years ago - 3 comments

#26 - Can this be used for lung x-ray segmentation too?

Issue - State: closed - Opened by bartmch almost 5 years ago - 1 comment

#25 - What is the max label for LTRCLobes_R231 segmentation?

Issue - State: closed - Opened by bartmch almost 5 years ago - 7 comments

#24 - mask.apply(image) not working

Issue - State: closed - Opened by Ralphchahwan almost 5 years ago - 1 comment

#23 - Empty segmentation after anaconda installation

Issue - State: closed - Opened by GiulioBen almost 5 years ago - 7 comments

#22 - Lung segmentation - extra segment outsize the body mass

Issue - State: closed - Opened by stergioc almost 5 years ago - 5 comments

#21 - --modeltype resunet not working

Issue - State: closed - Opened by GiulioBen almost 5 years ago - 1 comment

#20 - LTRCLobes_R231 model error

Issue - State: closed - Opened by nicolocardobi almost 5 years ago - 5 comments

#19 - ValueError: could not broadcast input array from shape (1989,4) into shape (1989,3)

Issue - State: closed - Opened by Alymostafa almost 5 years ago - 1 comment

#18 - Fuse models

Pull Request - State: closed - Opened by JoHof almost 5 years ago

#17 - Could you explain the hard code threshold

Issue - State: closed - Opened by Flyfoxs almost 5 years ago - 1 comment

#16 - Mask values in medicalsegmentation.com dataset

Issue - State: closed - Opened by ncovgt2020 almost 5 years ago - 2 comments

#15 - how about the training process and data?

Issue - State: closed - Opened by lancexiang almost 5 years ago - 2 comments

#14 - utils.py contains "import fill_voids" but the fill_voids.py is not available

Issue - State: closed - Opened by nadimpallipranav almost 5 years ago - 1 comment

#13 - Convert to tensorflow model

Issue - State: closed - Opened by Jorisfournel almost 5 years ago - 3 comments

#12 - Reshape error

Issue - State: closed - Opened by chengjianhong almost 5 years ago - 3 comments

#11 - Fix postprocess and rename module

Pull Request - State: closed - Opened by JoHof almost 5 years ago

#10 - A runtime error

Issue - State: closed - Opened by whalenr almost 5 years ago - 2 comments
Labels: help wanted

#9 - Problems about blog post ( map images back to HU)

Issue - State: closed - Opened by smallmax00 almost 5 years ago - 1 comment
Labels: question

#8 - [WIP] Mvp

Pull Request - State: closed - Opened by bkainz almost 5 years ago

#7 - the segmentation mask is an all black image

Issue - State: closed - Opened by aakash-saboo almost 5 years ago - 9 comments
Labels: bug

#6 - Fine Tune / retrain with more data ?

Issue - State: closed - Opened by Jorisfournel almost 5 years ago - 1 comment
Labels: question

#5 - deactivate background removal

Pull Request - State: closed - Opened by JoHof almost 5 years ago

GitHub / JoHof/lungmask issues and pull requests