# Give a thickness to the lumen

**URL:** <https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282>\
**Category:** Support\
**Created:** [September 1, 2020, 5:48pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282 "2020-09-01T17:48:40Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 1, 2020, 5:48pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/1 "2020-09-01T17:48:41Z")

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I extracted a Aorta lumen from a dicom files using 3d slicer, at this point I am looking for an open source software to give the lumen a desired thickness. if you know a software please leave a note.  
many thanks

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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:** [September 1, 2020, 5:49pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/2 "2020-09-01T17:49:30Z")

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You can use Hollow effect in Segment Editor module to create a thick shell from a solid segment.

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 12:02am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/3 "2020-09-02T00:02:17Z")

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Lassoan many thanks to you,It works perfect.  
and also is there any way in slicer 3D to make and add _ **cannula** _ (plastic tube using to bypass the left ventricular connecting it to the aorta in LVAD system) to the segmented aorta.  
Thanks again.

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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:** [September 2, 2020, 12:05am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/4 "2020-09-02T00:05:01Z")

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Yes, you can draw tubes using “Draw tube” effect in Segment editor. This effect is provided by SegmentEditorExtraEffects extension (you need to install this extension in Extension manager and restart Slicer).

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 12:33am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/5 "2020-09-02T00:33:51Z")

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I did it,but the Draw tube effect is not added to the editor! however some other effects are added like: fast marching, surface cut,split volume,watershed,…

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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:** [September 2, 2020, 12:43am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/6 "2020-09-02T00:43:49Z")

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Are you using latest Slicer Preview Release?

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 12:52am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/7 "2020-09-02T00:52:42Z")

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I am using 4.10.2 version

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 12:55am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/8 "2020-09-02T00:55:02Z")

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I see I am using stable, I just saw the preview version 4.11 in the website. Do I need to install 4.11?

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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:** [September 2, 2020, 12:56am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/9 "2020-09-02T00:56:12Z")

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Yes, the stable version is very old now, so it lacks many features and fixes, so I would recommend to use the most recent preview release.

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 12:57am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/10 "2020-09-02T00:57:18Z")

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Thank you so much. I’ll do and will be back to you if there is any issues.

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 2:39pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/11 "2020-09-02T14:39:55Z")

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Thank you Lassoan! The new release is perfect.  
I have a question:  
1-‘Hollow’ :how can I have the lumen and shell at the same time?  
when I make the shell with considering the current segment as inside surface,apparently the lumen vanishes.Is there any possibility to make shell and also hold the lumen in different color for visualization?

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**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 2:56pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/12 "2020-09-02T14:56:46Z")

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**"Draw tube" effect:** I don’t know how to use this effect in the point of connection(cannula to aorta shell) in order to make a neat and precise connection, and also is there any option to give them an angle in the connection point?  
when I make a cannula by Draw tube it seems it is connected to aorta in 3d but when I rotate the view It appears in different direction!

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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:** [September 2, 2020, 3:05pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/13 "2020-09-02T15:05:20Z")

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> [@Hamid](#):
>
> how can I have the lumen and shell at the same time?

You can make a copy of the segment (create a new segment and use Logical operators to copy content from other segment). [quote=“Hamid, post:12, topic:13282”]  
I don’t know how to use this effect in the point of connection(cannula to aorta shell) in order to make a neat and precise connection  
[/quote]

You can adjust the control points of the curve in any of the 3D views. Connection of a large-diameter tube can result in quite complex geometry, so maybe you need to clean up some edges or intersections using Paint effect.

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<div class="post-metadata">

**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 2, 2020, 4:40pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/14 "2020-09-02T16:40:45Z")

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Thanks for the great help!

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<div class="post-metadata">

**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 4, 2020, 3:47am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/15 "2020-09-04T03:47:43Z")

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I have 2 sets of DICOM files.one of them contains 150 images and other has 3000 images,both are the same CT-scan images and in the second one It seems like they are repeat themselves! and I am told the 2nd set is flow data.Is there any open source software to read flow data?

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<div class="post-metadata">

**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:** [September 4, 2020, 4:27am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/16 "2020-09-04T04:27:29Z")

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Recent Slicer Preview Releases should be able to read correctly many of the 4D flow data sets, but if you have problems with this one then share an anonymized/phantom/animal data set with us (upload the data set somewhere and post the link here) and we’ll investigate.

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<div class="post-metadata">

**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 6, 2020, 2:43am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/17 "2020-09-06T02:43:34Z")

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would you please tell me briefly which tabs or effects should be used to read the flow data? I have not done it before so I have no idea how the flow data will appear in 3d slicer from loading CT images. what form of data should be seen?

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<div class="post-metadata">

**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:** [September 6, 2020, 5:14am UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/18 "2020-09-06T05:14:02Z")

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You can load 4D data by switching to DICOM module, drag-and-dropping the DICOM folder to the Slicer application window, wait for the indexing to complete, then double-click on the patient, study, or series that you want to load.

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<div class="post-metadata">

**Author:** ![Hamid](https://avatars.discourse-cdn.com/v4/letter/h/5fc32e/32.png) [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Post date:** [September 6, 2020, 1:12pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/19 "2020-09-06T13:12:24Z")

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How can I extract e.g the ‘flow rate’ or any type of flow data from those data?

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<div class="post-metadata">

**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:** [September 6, 2020, 6:01pm UTC](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282/20 "2020-09-06T18:01:49Z")

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You can segment vessels and extract centerline using VMTK extension, straighten the vessel image and flow field using Curved planar reformat module (in Sandbox extension), and then get the average flow rate with a trivial Python script.

The main question is how the flow field can be imported from DICOM. It may need some tuning of the DICOM importer. We can help with this if you provide a sample data set (phantom, animal, or anonymized patient).

[Next page](https://discourse.slicer.org/t/give-a-thickness-to-the-lumen/13282.md?page=2)