Because 3D-Slicer software is unstable by systemic problem 3D slicer itself, It doesn't show 'Model' information and 'Run' button in Auto Segmentation option.

[ulphypro]

Hello, all developers!

A few days ago, it didn't show 'Model' information and 'Run' button in Auto Segmentation option while running 3D-Slicer 5.2.2 stable version, so I couldn't run Auto Segmentation in 3D-Slicer.

To solve this problem, I had installed Slicer-5.3.0-2023-03-19-linux-amd64.tar.gz preview version because of @SachidanandAlle, fortunately it ran well.

After spending 2 days, it occurred the problem again that don't show 'Model' information and 'Run' button in Auto Segmentation option in 3D-Slicer 5.3.0 preview version.

Despite I installed 'Slicer-5.3.0-2023-03-22-linux-amd64.tar.gz' preview version updated again, it didn't show 'Model' information and 'Run' button in Auto Segmentation option.

3D-Slicer software is unstable by systemic problem 3D slicer itself.

Please, update preview version of 3D Slicer software.

[lassoan]

3D-Slicer software is unstable by systemic problem 3D slicer itself.

3D Slicer is generally very stable and reliable. Of course all software have bugs that you may run into resuscitation if you do something a bit differently than most other users.

We fix all errors that we can reproduce and set can rarely fix problems that we cannot reproduce. Please describe how we can reproduce the issue (or provide screen recording) and include MONAI Label server and Slicer logs.

Nightly updates are only provided for the latest stable release (currently Slicer-5.2.2) or the very latest preview release, so use either of these versions (preferably the stable version).

[ulphypro]

Dear @lassoan

Thank you for answering my question.

[SachidanandAlle]

I tried the stable version just now.. and installed monailabel plugin from extension manager all looks good.
This is all fresh installation from scratch.

[ulphypro]

Dear @SachidanandAlle

Thank you for answering my question.

I installed slicer 5.2.2 stable version again and installed monailabel plugin (with 0.7.0rc3).

I installed all fresh.

But it didn't show 'Run' button in Auto Segmentation option.

What is the problem?

[SachidanandAlle]

When you have updated the model, likely the mode.pt (or trained model weights) are missing.
Normally inference is not enabled when you don't have pre-trained model or trained model. You should have at-least one of them in your apps/model

in your case.. either radiology/model/pretrained_segmentation.pt or radiology/model/segmentation.pt should exists.

[ulphypro]

@SachidanandAlle

segmentation.pt exists in apps/radiology/model folder.

[tangy5]

hi @ulphypro , I saw your screen shot, you are using a MRI image (BraTS data), but the "segmentation" model is a CT multi-organ segmentation model, I guess the issue could be that the workflow can't take MRI as input.
Can you try a CT scan? Thanks for trying 3D Slicer and MONAI Label.

[ulphypro]

Dear @tangy5

Thank you for answering my question.

Yes. I'm using MRI dataset. A few days ago, 'Run' button showed in Auto Segmentation option using MRI dataset after installing Slicer-5.3.0-2023-03-19-linux-amd64.tar.gz (preview version).

I downloaded MICAAI BraTS 2021 Challenge brain tumor dataset instead of Task01_BrainTumour dataset because 3D-Slicer only supported 1 channel. @diazandr3s recommended this solution. A number of t2_nii.gz files include in one folder.
MICCAI BraTS 2021 Challenge

If workflow can't take MRI as input, why do they use MRI sample datasets(ex: Task01_BrainTumour dataset, Task09_Spleen) in MONAILabel environment?

[SachidanandAlle]

Let's go step by step.. I see you have run some training etc.. let's forget all these things for a second.. and just try this.. 1. Download the radiology app for segmentation_spleen model 2. Start the server 3. Open the slicer and check if auto segmentation button works.

…

On Sun, Mar 26, 2023, 9:50 AM platanus ***@***.***> wrote: Dear @tangy5 <https://github.com/tangy5> Thank you for answering my question. Yes. I'm using MRI dataset. A few days ago, it showed 'Run' button in Auto Segmentation option using MRI dataset after installing Slicer 5.3.0 preview version. I downloaded MICAAI BraTS 2021 Challenge brain tumor dataset instead of Task01_BrainTumour dataset because 3D-Slicer only supported 1 channel. @diazandr3s <https://github.com/diazandr3s> recommended this solution. A number of t2_nii.gz files include in one folder as following. MICCAI BraTS 2021 Challenge <http://braintumorsegmentation.org/> If workflow can't take MRI as input, why do they use MRI sample datasets(ex: Task01_BrainTumour dataset, Task00_Spleen) in MONAILabel environment? — Reply to this email directly, view it on GitHub <#1357 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABX7YK3KPRR5KSRLRLCG6B3W6BXUXANCNFSM6AAAAAAWGHOUGU> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[ulphypro]

Dear @SachidanandAlle

Thank you for helping me.

Despite I ran as above step by step, 'Run' button don't show in Auto Segmentation option.

Can you show 'Run' buttion in Auto Segmentation well in Slicer 5.2.2 stable version based on monailabel 0.7.0rc3?

[SachidanandAlle]

and what is the output when you open this url in your browser: http://127.0.0.1:8000/info/

[ulphypro]

@SachidanandAlle

The information is as following.

[SachidanandAlle]

This is definitely weird.. I don't know if you are having multiple 3D Slicer versions on the same box which is causing this behavior.
If possible you can try from another node/box and connect to the same server.. otherwise I don't see any issue with monailabel server here..
from the above json, i can see you have a model segmentation_spleen for running auto segmentation..

[ulphypro]

@SachidanandAlle

So, can you show 'Run' button in Auto Segmentation using slicer 5.2.2. stable?
What is difference between monailabel 0.7.0rc3(me) and 0.7.0rc3+1(you)?

[SachidanandAlle]

try the latest version.. but this problem is not related to monailabel version. I can already see monailabel output is good.
and yes, i have verified on slicer release and shared those snapshots..

but you can go head and update the monailable version to rc3 (there are some other fixes added in rc3)

have u also tried uninstalling existing plugin and configure monailabel plugin via developer mode.. (github source)
https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/slicer#install-plugin-in-developer-mode

[ulphypro]

Dear @SachidanandAlle

When I installed 5.3.0 preview version uploaded by 2023-03-26, the file name is Slicer-5.3.0-2023-03-22-linux-amd64.tar.gz. Isn't it Slicer-5.3.0-2023-03-25-linux-amd64.tar.gz?

I already had installed slicer 5.3.0 preview version uploaded by 2023-03-23, it couldn't show run button in Auto Segmentation option.

[ulphypro]

@SachidanandAlle

I can't show 'Run' button in Auto Segmentation option despite I tried to run with all methods that installed preview (and stable) version of slicer, reinstalled MONAILabel module and reinstalled monailabel==0.7.0rc3.

I don't know why 'Run' button can't show in Auto Segmentation option from only me.

[ulphypro]

Dear all developers!

A few days ago, when I had run slicer 5.3.0(edited 2023-03-19) based on monailabel 0.6.0, 'Run' button showed in Auto Segmentation option.

But despite I had run it again after a few days, 'Run' button couldn't show in Auto Segmentation option.

So I reinstalled updated MONAILabel module, monailabel==0.7.0rc3 and Slicer 5.3.0(updated 2023-03-26 or 2023-03-28), but 'Run' button couldn't show in Auto Segmentation option.

I don't know why this problem occurs from only me.

I don't know how to solve this problem.

Please, help me to solve this problem.

[SachidanandAlle]

have you tried running slicer from a different machine.. u can keep monailabel on same box.. just try running 3D slicer from another box..

[tangy5]

From your above screenshot here:

I saw there is no model shown, and the "run" is greyed out.

0. Check the 3D Slicer "Edit", then "settings", "MONAI Label". Should look like this, check developer mode.
   
   You can also, "restore defaults", reinstall MONAI Label plugin.

Other suggestions:

1. Can you try clicking the model and see whether there are models available in the drop-down scroll
2. Click the 3D Slicer "view" panel on the top, and check the "error log". See if there is useful information
3. Check MONAI Label terminal logs, whether the "inferer" is added.

[ulphypro]

Dear @tangy5

Thank you for answering my question.

I checked process log when I had run using 3D Slicer based on monailabel.
The log information is as following.

---

Other sugesstions:

1. Can you try clicking the model see whether there are models available in the drop-down scroll.
   ----> I can't clicking the model because 'Model' is empty.

2. Click the 3D Slicer "view" panel on the top, and check the "error log". See if there is useful information
   ---->error log
   

4. Check MONAI Label terminal logs, whether the "inferer" is added.

---> <MONAILabel terminal log information that "inferer" added

(monailabel-env) trl@trl-workstation:~$ monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models segmentation_spleen
Using PYTHONPATH=/home/trl/anaconda3/envs:

Failed to load image Python extension: '/home/trl/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/torchvision/image.so: undefined symbol: _ZN3c104cuda20CUDACachingAllocator9allocatorE'If you don't plan on using image functionality from torchvision.io, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you have libjpeg or libpng installed before building torchvision from source?
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: version = False
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: app = /home/trl/apps/radiology
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: studies = /home/trl/datasets/Task09_Spleen/imagesTr
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: verbose = INFO
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: conf = [['models', 'segmentation_spleen']]
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: host = 0.0.0.0
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: port = 8000
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: uvicorn_app = monailabel.app:app
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: ssl_keyfile = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: ssl_certfile = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: ssl_keyfile_password = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: ssl_ca_certs = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: workers = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: limit_concurrency = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: access_log = False
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: log_config = None
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: dryrun = False
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:282) - USING:: action = start_server
[2023-03-29 14:39:49,637] [87307] [MainThread] [INFO] (main:293) -
Allow Origins: ['']
[2023-03-29 14:39:49,814] [87307] [MainThread] [INFO] (uvicorn.error:75) - Started server process [87307]
[2023-03-29 14:39:49,815] [87307] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-03-29 14:39:49,815] [87307] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /home/trl/apps/radiology; studies: /home/trl/datasets/Task09_Spleen/imagesTr; conf: {'models': 'segmentation_spleen'}
[2023-03-29 14:39:49,843] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-03-29 14:39:49,844] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2023-03-29 14:39:49,845] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-03-29 14:39:49,846] [87307] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-03-29 14:39:49,846] [87307] [MainThread] [INFO] (main:93) - +++ Adding Model: segmentation_spleen => lib.configs.segmentation_spleen.SegmentationSpleen
[2023-03-29 14:39:49,846] [87307] [MainThread] [INFO] (monailabel.utils.others.generic:184) - Downloading resource: /home/trl/apps/radiology/model/pretrained_segmentation_spleen.pt from https://github.com/Project-MONAI/MONAILabel/releases/download/pretrained/radiology_segmentation_unet_spleen.pt
pretrained_segmentation_spleen.pt: 18.4MB [00:04, 4.78MB/s]
2023-03-29 14:39:53,889 - INFO - Downloaded: /home/trl/apps/radiology/model/pretrained_segmentation_spleen.pt
2023-03-29 14:39:53,889 - INFO - Expected md5 is None, skip md5 check for file /home/trl/apps/radiology/model/pretrained_segmentation_spleen.pt.
[2023-03-29 14:39:54,913] [87307] [MainThread] [INFO] (lib.configs.segmentation_spleen:75) - EPISTEMIC Enabled: False; Samples: 5
[2023-03-29 14:39:54,913] [87307] [MainThread] [INFO] (main:96) - +++ Using Models: ['segmentation_spleen']
[2023-03-29 14:39:54,913] [87307] [MainThread] [INFO] (monailabel.interfaces.app:134) - Init Datastore for: /home/trl/datasets/Task09_Spleen/imagesTr
[2023-03-29 14:39:54,913] [87307] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['.nii.gz', '.nii', '.nrrd', '.jpg', '.png', '.tif', '.svs', '*.xml']
[2023-03-29 14:39:54,925] [87307] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2023-03-29 14:39:54,925] [87307] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-03-29 14:39:54,933] [87307] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: segmentation_spleen => <lib.infers.segmentation_spleen.SegmentationSpleen object at 0x7f14081d96d0>
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (main:191) - {'segmentation_spleen': <lib.infers.segmentation_spleen.SegmentationSpleen object at 0x7f14081d96d0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7f140812be20>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7f1407dc6d30>}
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: segmentation_spleen => <lib.trainers.segmentation_spleen.SegmentationSpleen object at 0x7f1407dc6e20>
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/trl/.cache/monailabel/sessions
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (monailabel.interfaces.app:468) - App Init - completed
[2023-03-29 14:39:54,934] [timeloop] [INFO] Starting Timeloop..
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-03-29 14:39:54,934] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f1408147e50>
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x7f1408147e50>
[2023-03-29 14:39:54,934] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2023-03-29 14:39:54,934] [87307] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)

[lassoan]

If you want to directly see what is happening and why, then you can attach a debugger and step through the code. It may take just few minutes.

[ulphypro]

Dear @lassoan

Thank you for answering my question.

I'll check referring your answer.

[ulphypro]

Dear @SachidanandAlle

Thank you for answering my question.

I ran 3D slicer based on MONAILabel in other PC.

'Run' button couldn't also show in Auto Segmentation option when I had run 3D Slicer based on MONAILabel in other PC..

[SachidanandAlle]

Since this is heading no where.. I suggest @ulphypro and @tangy5 can have a video call and fix this one for all..

There are many users using the monailabel + 3D slicer setup but no one had such issue. Even some are using regularly in their labs.
Something is missing here on your setup..

[ulphypro]

Dear @SachidanandAlle

Thank you for answering my question.

I often occurred this problem that didn't show 'Run' button in Auto Segmentation option. When I reinstalled updated 3D Slicer software, sometimes Run button could show in Auto Segmentation option.

During December 15, 2022 to March 20, 2023, I tried to install MONAILabel module, monailabel==0.6.0 package, and Slicer software preview version for solving the problem again and again.

And I ran monailabel server "monailabel start_server --app apps/radiology --studies datasets/BraTS2021_Training_Data/brats --conf models segmentation"

By the way, I had only installed Slicer 5.3.0-2023-03-20 preview version on March 20, 2023, Run button did show in Auto Segmentation.

I installed module and package as following before I had run 3D Slicer based on MONAILabel and modified /apps/radiology/lib/configs/segmentation.py code.

In Linux(Ubuntu 22.04 LTS) OS environment

1. MONAILabel module installation

2. Package installation of /MONAILabel/requirements.txt

3. monailabel 0.7.0rc3 package

4. Package installation of torch+cuda11.8

5. Download /apps/radiology

6. Installation of updated Slicer preview version(2023-03-28) or stable version(2023-02-22)

7. modification of /apps/radiology/lib/configs/segmentation.py code
   (1) code modification
   --># Labels
   self.labels = {
   "tumor": 1,

    } 
   

(2) code modification
---># Download PreTrained Model
if strtobool(self.conf.get("use_pretrained_model", "false")):

And then I run monailabel server "monailabel start_server --app apps/radiology --studies datasets/BraTS2021_Training_Data/brats --conf models segmentation"

Is here the problem in installation procedure above?

Are you planing to update Slicer software this weekend?

Then, I'll try to check whether Run shows in Auto Segmentation option or not.

And... I'll send the email to @tangy5.

[tangy5]

@ulphypro , please email [email protected] for further communication with the Org and co-op.

[ulphypro]

Dear @tangy5

Thank you for informing your email address.

I sent the email to you.

Please, check your email.