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Unable to display http://127.0.0.1:8080/ on a browser (Mac, Windows), error on Linux host (Ubuntu). #23

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julfou81 opened this issue Feb 27, 2025 · 4 comments
Open

Unable to display http://127.0.0.1:8080/ on a browser (Mac, Windows), error on Linux host (Ubuntu). #23

julfou81 opened this issue Feb 27, 2025 · 4 comments

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@julfou81
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julfou81 commented Feb 27, 2025 •
edited
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Hi,

Thank you very much for sharing this nice tool! Congratulations also for the nice documentation!
I tried to use it with the docker image and did not succeed yet in making it work.

In fact everything seems to be working nicely, except the display through http://127.0.0.1:8080.
I can see that the images are seen and processed with 3dvolreg and no error message appears in the Docker log file.
However when I put the address http://127.0.0.1:8080 , I get an error message : "Firefox can't connect with the server at address 127.0.0.1:8080.".
I tried with several web browsers and no success.
I got to this point on two hosts: Windows 11 and MacBook Pro M1 15.2.

Here is the command I used on my mac for instance:

run  -e SCANBUDDY_PASS -e SCANBUDDY_SESSION_KEY --user 1000:1000 --network host -v /Users/jsein/Documents/Centre_IRMf/DATA/Scanbuddy:/data ghcr.io/harvard-nrg/scanbuddy:latest --folder /data --config /data/scanbuddy.yaml

Here is the Docker file log:

docker run  -e SCANBUDDY_PASS -e SCANBUDDY_SESSION_KEY --user 1000:1000 --network host -v /Users/jsein/Documents/Centre_IRMf/DATA/Scanbuddy:/data ghcr.io/harvard-nrg/scanbuddy:latest --folder /data --config /data/scanbuddy.yaml  
INFO:scanbuddy.watcher.directory:starting directory watcher on /data
┌────────────────┬──────────────────────────────────────────────┐
│ Platform       │ Linux-6.5.11-linuxkit-aarch64-with-glibc2.28 │
├────────────────┼──────────────────────────────────────────────┤
│ Processor      │ aarch64                                      │
├────────────────┼──────────────────────────────────────────────┤
│ Python version │ 3.13.2                                       │
├────────────────┼──────────────────────────────────────────────┤
│ GIL enabled    │ False                                        │
└────────────────┴──────────────────────────────────────────────┘
Dash is running on http://127.0.0.1:8080/

INFO:dash.dash:Dash is running on http://127.0.0.1:8080/

 * Serving Flask app 'fMRI Motion'
 * Debug mode: off
INFO:scanbuddy.watcher.dicom:starting dicom watcher on /data/dicom1
INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0225 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.03375 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 936518
WARNING:retry.api:, retrying in 0.050625 seconds...
INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:found first series instance uid 1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom1/52453120.dcm to /data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453120.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453120.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453120.dcm",
      "volreg": null,
      "nii_path": null
    }
  ]
]
WARNING:scanbuddy.proc.volreg:the two input dicom files are the same. registering 52453120.dcm to itself will yield 0s
INFO:scanbuddy.proc.volreg:volreg array from registering volume 1 to volume 1: [np.float64(-0.0), np.float64(-0.0), np.float64(-0.0), np.float64(-0.0), np.float64(-0.0), np.float64(-0.0)]
INFO:scanbuddy.proc.volreg:processing took 0.2323148250579834 seconds
INFO:scanbuddy.proc.params:checking if ('HeadNeck_64', 'HC1-6') == ('Head_32', 'HEA')
INFO:scanbuddy.proc.params:checking if ('HeadNeck_64', 'HC1-6') == ('Head_32', 'HEP')
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 1
INFO:scanbuddy.proc.snr:extracting fdata from volume 1 took 0.019835948944091797 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets Banco2025, Session: 2025.01.23-09:03:56-STD-1.3.12.2.1107.5.99.3, Series: task-FormantSaliency_run1_bold, Scan Number: 36, Date & Time: 2025-02-27 17:08:03
INFO:scanbuddy.proc:shape of zeros: (100, 100, 36, 441)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 36, 1)
INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0225 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.03375 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 936502
WARNING:retry.api:, retrying in 0.050625 seconds...
INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom1/52453131.dcm to /data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453131.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453131.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453120.dcm",
      "volreg": [
        -0.0,
        -0.0,
        -0.0,
        -0.0,
        -0.0,
        -0.0
      ],
      "nii_path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/bold_1.nii"
    }
  ]
]
INFO:scanbuddy.proc.volreg:volreg array from registering volume 2 to volume 1: [np.float64(0.0272), np.float64(-0.0081), np.float64(0.0221), np.float64(0.0067), np.float64(0.0157), np.float64(-0.014)]
INFO:scanbuddy.proc.volreg:processing took 0.2503972053527832 seconds
INFO:scanbuddy.proc.params:already checked an instance from series 36
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 2
INFO:scanbuddy.proc.snr:extracting fdata from volume 2 took 0.02746725082397461 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets Banco2025, Session: 2025.01.23-09:03:56-STD-1.3.12.2.1107.5.99.3, Series: task-FormantSaliency_run1_bold, Scan Number: 36, Date & Time: 2025-02-27 17:08:09
INFO:scanbuddy.proc:shape of zeros: (100, 100, 36, 441)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 36, 1)
INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0225 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.03375 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 936528
WARNING:retry.api:, retrying in 0.050625 seconds...
INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom1/52453142.dcm to /data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453142.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453142.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/52453131.dcm",
      "volreg": [
        0.0272,
        -0.0081,
        0.0221,
        0.0067,
        0.0157,
        -0.014
      ],
      "nii_path": "/data/dicom1/1.3.12.2.1107.5.2.43.66072.30000025012308492889500000003/1.3.12.2.1107.5.2.43.66072.2025012309535149720428997.0.0.0/bold_2.nii"
    }
  ]
]
INFO:scanbuddy.proc.volreg:volreg array from registering volume 3 to volume 2: [np.float64(0.0409), np.float64(-0.0077), np.float64(-0.0125), np.float64(-0.0103), np.float64(0.0589), np.float64(-0.0029)]
INFO:scanbuddy.proc.volreg:processing took 0.23663830757141113 seconds
INFO:scanbuddy.proc.params:already checked an instance from series 36
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 3
INFO:scanbuddy.proc.snr:extracting fdata from volume 3 took 0.025267601013183594 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets Banco2025, Session: 2025.01.23-09:03:56-STD-1.3.12.2.1107.5.99.3, Series: task-FormantSaliency_run1_bold, Scan Number: 36, Date & Time: 2025-02-27 17:08:22
INFO:scanbuddy.proc:shape of zeros: (100, 100, 36, 441)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 36, 1)

Do you have any suggestions on what test to run to solve this issue?

On the contrary, when I tried on a Linux System (Ubuntu 18.04.6) and in this case the display on http://127.0.0.1:8080 works but there is an issue with the program itself. Here is the docker log in that case:

docker run -d  -e SCANBUDDY_PASS -e SCANBUDDY_SESSION_KEY --user 1000:1000 --network host -v /DATA1/Scanbuddy:/data ghcr.io/harvard-nrg/scanbuddy:latest --folder /data --config /data/scanbuddy.yaml
2caa2c3c6fefe00ab3672a46c1fe16288f96d2cdc32e710d1ac3b3ea4d522d0c
(base) photon@mri-server:~/Downloads$ docker container ls
CONTAINER ID   IMAGE                                  COMMAND                  CREATED          STATUS          PORTS                                                 NAMES
2caa2c3c6fef   ghcr.io/harvard-nrg/scanbuddy:latest   "mamba run -n python…"   12 seconds ago   Up 11 seconds                                                         great_panini
85a917f1db70   redis/redis-stack:latest               "/entrypoint.sh"         8 hours ago      Up 8 hours      6379/tcp, 0.0.0.0:8001->8001/tcp, :::8001->8001/tcp   redis
(base) photon@mri-server:~/Downloads$ docker container logs  2caa2c3c6fef
INFO:scanbuddy.watcher.directory:starting directory watcher on /data
┌────────────────┬───────────────────────────────────────────────┐
INFO:dash.dash:Dash is running on http://127.0.0.1:8080/

│ Platform       │ Linux-5.4.0-150-generic-x86_64-with-glibc2.28 │
├────────────────┼───────────────────────────────────────────────┤
│ Processor      │ x86_64                                        │
├────────────────┼───────────────────────────────────────────────┤
│ Python version │ 3.13.2                                        │
├────────────────┼───────────────────────────────────────────────┤
│ GIL enabled    │ False                                         │
└────────────────┴───────────────────────────────────────────────┘
Dash is running on http://127.0.0.1:8080/

 * Serving Flask app 'fMRI Motion'
 * Debug mode: off
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/



/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

Thank you very much for your help!
@dmd
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dmd commented Feb 27, 2025

Docker does not support --network host on anything but Linux.

@julfou81
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Author

Thank you for the quick reply! This makes a lot of sense then ;-).

I still have the issue on Ubuntu 18.04.6, is this version too old?

@dmd
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Contributor

dmd commented Feb 27, 2025

I'll defer to the authors on everything else :)

@julfou81
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julfou81 commented Feb 27, 2025 •
edited
Loading

Actually with the newer docker version (v 4.38.0) , host networking is possible on mac!

Image

Now I can see the display but not yet the motion curves.

Here is the Docker log:

docker run  -e SCANBUDDY_PASS -e SCANBUDDY_SESSION_KEY --user 1000:1000 --network=host  -v /Users/jsein/Documents/Centre_IRMf/DATA/Scanbuddy:/data ghcr.io/harvard-nrg/scanbuddy:latest --folder /data --config /data/scanbuddy.yaml  
INFO:scanbuddy.watcher.directory:starting directory watcher on /data
┌────────────────┬──────────────────────────────────────────────┐
│ Platform       │ Linux-6.12.5-linuxkit-aarch64-with-glibc2.28 │
├────────────────┼──────────────────────────────────────────────┤
│ Processor      │ aarch64                                      │
├────────────────┼──────────────────────────────────────────────┤
│ Python version │ 3.13.2                                       │
├────────────────┼──────────────────────────────────────────────┤
│ GIL enabled    │ False                                        │
└────────────────┴──────────────────────────────────────────────┘
Dash is running on http://127.0.0.1:8080/

INFO:dash.dash:Dash is running on http://127.0.0.1:8080/

 * Serving Flask app 'fMRI Motion'
 * Debug mode: off
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/


*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable

INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0225 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.03375 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.050625 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0759375 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.11390625000000001 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 1696720
WARNING:retry.api:, retrying in 0.17085937500000004 seconds...
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:found first series instance uid 1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom2/77974426.dcm to /data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974426.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974426.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974426.dcm",
      "volreg": null,
      "nii_path": null
    }
  ]
]
WARNING:scanbuddy.proc.volreg:the two input dicom files are the same. registering 77974426.dcm to itself will yield 0s
INFO:scanbuddy.proc.volreg:volreg array from registering volume 1 to volume 1: [np.float64(-0.0), np.float64(-0.0), np.float64(0.0), np.float64(-0.0), np.float64(-0.0), np.float64(0.0)]
INFO:scanbuddy.proc.volreg:processing took 0.4681205749511719 seconds
INFO:scanbuddy.proc.params:checking if ('HeadNeck_64', 'HC1-7') == ('Head_32', 'HEA')
INFO:scanbuddy.proc.params:checking if ('HeadNeck_64', 'HC1-7') == ('Head_32', 'HEP')
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 1
INFO:scanbuddy.proc.snr:extracting fdata from volume 1 took 0.03186917304992676 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets PhantomPainBrain, Session: 2025.02.26-09:13:54-STD-1.3.12.2.1107.5.99.3, Series: task-VibStim_run4_bold, Scan Number: 84, Date & Time: 2025-02-27 18:30:11
INFO:scanbuddy.proc:shape of zeros: (100, 100, 70, 360)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 70, 1)
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/


INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 1696928
WARNING:retry.api:, retrying in 0.0225 seconds...
INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom2/77974437.dcm to /data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974437.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974437.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974426.dcm",
      "volreg": [
        -0.0,
        -0.0,
        0.0,
        -0.0,
        -0.0,
        0.0
      ],
      "nii_path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/bold_1.nii"
    }
  ]
]
INFO:scanbuddy.proc.volreg:volreg array from registering volume 2 to volume 1: [np.float64(0.0136), np.float64(-0.0635), np.float64(0.0119), np.float64(0.0274), np.float64(0.0018), np.float64(-0.0563)]
INFO:scanbuddy.proc.volreg:processing took 0.4021797180175781 seconds
INFO:scanbuddy.proc.params:already checked an instance from series 84
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 2
INFO:scanbuddy.proc.snr:extracting fdata from volume 2 took 0.04758882522583008 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets PhantomPainBrain, Session: 2025.02.26-09:13:54-STD-1.3.12.2.1107.5.99.3, Series: task-VibStim_run4_bold, Scan Number: 84, Date & Time: 2025-02-27 18:30:19
INFO:scanbuddy.proc:shape of zeros: (100, 100, 70, 360)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 70, 1)
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/


INFO:scanbuddy.watcher.dicom:file size was -1
INFO:scanbuddy.watcher.dicom:file size is now 0
WARNING:retry.api:, retrying in 0.01 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.015 seconds...
WARNING:retry.api:File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading., retrying in 0.0225 seconds...
INFO:scanbuddy.watcher.dicom:file size was 0
INFO:scanbuddy.watcher.dicom:file size is now 1696964
WARNING:retry.api:, retrying in 0.03375 seconds...
INFO:scanbuddy.watcher.dicom:single echo scan detected
INFO:scanbuddy.watcher.dicom:moving file from /data/dicom2/77974448.dcm to /data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0
INFO:scanbuddy.watcher.dicom:publishing message to topic=incoming with ds=/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974448.dcm
INFO:scanbuddy.proc.volreg:received tasks for volume registration
INFO:scanbuddy.proc.volreg:[
  [
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974448.dcm",
      "volreg": null,
      "nii_path": null
    },
    {
      "path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/77974437.dcm",
      "volreg": [
        0.0136,
        -0.0635,
        0.0119,
        0.0274,
        0.0018,
        -0.0563
      ],
      "nii_path": "/data/dicom2/1.3.12.2.1107.5.2.43.66072.30000025022608042500800000005/1.3.12.2.1107.5.2.43.66072.2025022611205891214300442.0.0.0/bold_2.nii"
    }
  ]
]
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

INFO:scanbuddy.proc.volreg:volreg array from registering volume 3 to volume 2: [np.float64(-0.0111), np.float64(0.0493), np.float64(0.0102), np.float64(-0.0166), np.float64(0.0065), np.float64(0.1115)]
INFO:scanbuddy.proc.volreg:processing took 0.39647650718688965 seconds
INFO:scanbuddy.proc.params:already checked an instance from series 84
INFO:scanbuddy.proc.snr:received tasks for fdata extraction
INFO:scanbuddy.proc.snr:extracting fdata for volume 3
INFO:scanbuddy.proc.snr:extracting fdata from volume 3 took 0.042696237564086914 seconds
INFO:scanbuddy.proc:Scan info: Project: Projets PhantomPainBrain, Session: 2025.02.26-09:13:54-STD-1.3.12.2.1107.5.99.3, Series: task-VibStim_run4_bold, Scan Number: 84, Date & Time: 2025-02-27 18:30:25
INFO:scanbuddy.proc:shape of zeros: (100, 100, 70, 360)
INFO:scanbuddy.proc:shape of first slice means: (100, 100, 70, 1)
WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

WARNING:scanbuddy.view.dash:unable to get messages from message broker, service unavailable
/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/

/sw/miniforge/envs/python3.13t/lib/python3.13t/site-packages/_plotly_utils/basevalidators.py:2596: DeprecationWarning:

*scattermapbox* is deprecated! Use *scattermap* instead. Learn more at: https://plotly.com/python/mapbox-to-maplibre/
...

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@dmd @julfou81