# ABL Temporal Bone Segmentation Module

**URL:** <https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [March 12, 2021, 2:37pm UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494 "2021-03-12T14:37:57Z")\
**Posts on this page:** 13\
**Page:** 1

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [March 12, 2021, 2:37pm UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/1 "2021-03-12T14:37:57Z")

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Dear Andras @lassoan .  
I posted this topic 1 month ago. I’m segmenting temporal bone using ABL Temporal Bone Segmentation. I stuck at step 2: Rigid registration because the my data and atlas is too far off (Too many samples map outside moving image buffer: 188 / 1117). I’ve installed SlicerElastix, Slicer version 4.11.20200930.  
Can you make a detailed YouTube video on how to automatically segment temporal bone? This is really important to me. I very appreciate your help. Thank you.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/a/ba38fdd57c2d745680abf78370781d94dd775175.png)

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [June 10, 2021, 2:34am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/2 "2021-06-10T02:34:43Z")

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Dear @lassoan  
I’ve completed rigid registration. For the next step, can you show me the address or link of ABL inference or Docker host? I can’t find it. There are some lines of ABL inference code on Github but I don’t know how to use.  
I appreciate your help very much. Thank you.  
Best regards.  
 ![04a_inferenceremote](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/a/ca4231187abe53b55f616650b242ad1f39e909bf.png)  
 ![20210610_060938](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/f/ef87521ef0a523aa52e8cce338d3f1dee2a72000.png)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 10, 2021, 11:42pm UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/3 "2021-06-10T23:42:08Z")

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I don’t know much about this extension. I would recommend to submit an issue to their repository (and copy the issue number here for reference).

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**Author:** ![Johann](https://avatars.discourse-cdn.com/v4/letter/j/54ee81/32.png) [@Johann](https://discourse.slicer.org/u/Johann)\
**Post date:** [June 14, 2021, 1:24pm UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/4 "2021-06-14T13:24:22Z")

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Hi @lassoan and @DAT_Minh.  
I run inference and the process stopped at 30%. Here’s the message log:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/7/d708d9a4cfd4f9bd497190f35c76c789450bb01b.png)  
Does it contain issue number? Can you debug the code from docker?

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 17, 2021, 3:58am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/5 "2021-06-17T03:58:18Z")

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Have you set up the required server as described [here](https://github.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation#dependencies) in the extension’s documentation?

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [June 20, 2021, 4:55am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/6 "2021-06-20T04:55:15Z")

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I don’t know how to set up the server. Can you make a video? Thank you @lassoan

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 20, 2021, 11:18am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/7 "2021-06-20T11:18:34Z")

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Setup instructions are available at the link in my previous post. I have never set up the server myself, so I cannot give any more specific information.

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [June 20, 2021, 11:57pm UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/8 "2021-06-20T23:57:38Z")

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Thank you. I followed the instruction but don’t know how to do

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 21, 2021, 12:36am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/9 "2021-06-21T00:36:27Z")

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I would recommend to submit this question as an issue to the extension’s repository. Describe what steps you performed and at what point you got stuck (what you did, what you expected to happen, and what happened instead). Post here a link to the submitted issue so that people who will run into the same issue in the future can find how the problem got resolved.

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**Author:** ![FUFU](https://avatars.discourse-cdn.com/v4/letter/f/50afbb/32.png) [@FUFU](https://discourse.slicer.org/u/FUFU)\
**Post date:** [September 13, 2022, 9:06am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/10 "2022-09-13T09:06:25Z")

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hello I also met the trouble .Can you tell me how to solve it ? thank you.Error:  
My problem is  
 ![1663059954099](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/6/56d2bd23ee6c091804d1b8b4348f60ef13422e7c.png)  
Command ‘elastix’ returned non-zero exit status 1.

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**Author:** ![Young\_Wang](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/young_wang/32/13926_2.png) [@Young\_Wang](https://discourse.slicer.org/u/Young_Wang)\
**Post date:** [December 1, 2022, 12:34am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/12 "2022-12-01T00:34:36Z")

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hi @Johann, i wonder if you have figured it out how to use this extension?

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**Author:** ![evan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/evan/32/4953_2.png) [@evan](https://discourse.slicer.org/u/evan)\
**Post date:** [December 10, 2022, 12:00am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/13 "2022-12-10T00:00:59Z")

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Reference to the GitHub Issue used to track the issue that @DAT_Minh mentioned:

> <https://github.com/Auditory-Biophysics-Lab/Slicer-ABLTemporalBoneSegmentation/issues/8>
>
> I was excited when I found out about this module, and thank you for all your wor…k. Currently I'm stuck at step 2 and I got the error message saying: 
> "command elsatix return to non-zero exit status 1 error."
> 
> \<img width="1503" alt="Screenshot 2022-11-30 at 14 18 11" src="https://user-images.githubusercontent.com/61168470/204880516-399145d8-ca63-4acb-aed8-c750e1a850d9.png"\>
> 
> Any help is greatly appreciated. 
> @ben-connors @jamesobutler @e-simpson

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**Author:** ![DR.DHARAM\_SINGH\_RATH](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dr.dharam_singh_rath/32/66051_2.png) [@DR.DHARAM\_SINGH\_RATH](https://discourse.slicer.org/u/DR.DHARAM_SINGH_RATH)\
**Post date:** [May 22, 2023, 6:39am UTC](https://discourse.slicer.org/t/abl-temporal-bone-segmentation-module/16494/14 "2023-05-22T06:39:36Z")

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Can anyone help? Even after hardening doing everything not able to segment can anyone solve this issue create a video to solve this issue let me inform I am it is very useful extension only we are not able to go beyond 7 per cent after rigid registration step2

itk::ExceptionObject (0x7fdbb6707300)

Location: “ElastixTemplate - Run()”

File: /Volumes/D/S/S-0-E-b/SlicerElastix-build/elastix/Common/CostFunctions/itkAdvancedImageToImageMetric.hxx

Line: 916

Description: ITK ERROR: AdvancedMattesMutualInformationMetric(0x7fdbb701aa00): Too many samples map outside moving image buffer: 48 / 1117

Error occurred during actual registration.

Errors occurred!

Error: Command ‘elastix’ returned non-zero exit status 1.