# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=172

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

**Page:** 173

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## [3d slicer and embolism](https://discourse.slicer.org/t/3d-slicer-and-embolism/27613)

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**Author:** [@17banai99](https://discourse.slicer.org/u/17banai99)\
**Replies:** 0\
**Last updated:** [February 3, 2023, 12:23pm UTC](https://discourse.slicer.org/t/3d-slicer-and-embolism/27613 "2023-02-03T12:23:20Z")

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Has anyone ever worked with the 3d Slicer to highlight pulmonary embolism? If so, is it more efficient than the usual means.

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## [3D Slicer closes when sending images from the tomograph](https://discourse.slicer.org/t/3d-slicer-closes-when-sending-images-from-the-tomograph/25507)

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**Author:** [@Baez](https://discourse.slicer.org/u/Baez)\
**Replies:** 0\
**Last updated:** [October 1, 2022, 1:39am UTC](https://discourse.slicer.org/t/3d-slicer-closes-when-sending-images-from-the-tomograph/25507 "2022-10-01T01:39:24Z")

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Hello. My question is why when I send a tomography study to the DICOM service, does Slicer3D close? could someone tell me something about it? Thank you.

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## [Heatmap of Brain](https://discourse.slicer.org/t/heatmap-of-brain/25439)

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**Author:** [@lsprs](https://discourse.slicer.org/u/lsprs)\
**Replies:** 0\
**Last updated:** [September 26, 2022, 4:27pm UTC](https://discourse.slicer.org/t/heatmap-of-brain/25439 "2022-09-26T16:27:56Z")

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Hello, I’m interested in finding a way to compare the volume distribution of the brain for patients with various conditions. My plan is to: Obtain CT heads Strip the skull Segment the brain Dynamically visualize the …

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## [Annotate DICOM videos](https://discourse.slicer.org/t/annotate-dicom-videos/24713)

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**Author:** [@pmpradhan](https://discourse.slicer.org/u/pmpradhan)\
**Replies:** 1\
**Last updated:** [March 21, 2023, 2:11am UTC](https://discourse.slicer.org/t/annotate-dicom-videos/24713 "2023-03-21T02:11:38Z")

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Operating system: Windows Slicer version:4.11.20210226 Expected behavior: Annotate one frame and have it across all other frames for a single study. Actual behavior: Can annotate one frame and save it but cannot have …

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## [How to distinguish between skeletal muscle and adipose tissue](https://discourse.slicer.org/t/how-to-distinguish-between-skeletal-muscle-and-adipose-tissue/24488)

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**Author:** [@yoyowang](https://discourse.slicer.org/u/yoyowang)\
**Replies:** 0\
**Last updated:** [July 25, 2022, 8:11pm UTC](https://discourse.slicer.org/t/how-to-distinguish-between-skeletal-muscle-and-adipose-tissue/24488 "2022-07-25T20:11:54Z")

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## [Profile of Hounsfield Units for each pixel](https://discourse.slicer.org/t/profile-of-hounsfield-units-for-each-pixel/21758)

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**Author:** [@Michel\_Atieh](https://discourse.slicer.org/u/Michel_Atieh)\
**Replies:** 1\
**Last updated:** [March 21, 2023, 1:59am UTC](https://discourse.slicer.org/t/profile-of-hounsfield-units-for-each-pixel/21758 "2023-03-21T01:59:31Z")

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Hello, in radiation therapy we are very interested in knowing the profile of the Hounsfield Units(HUs) of the pixels of our CT scans. In ImageJ (ImageJ) we can get the profile of the HUs with a simple (ctrl + k). Is t…

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## [Can VolumeReconstructor function run on GPU?](https://discourse.slicer.org/t/can-volumereconstructor-function-run-on-gpu/21257)

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**Author:** [@Junshi\_Peng](https://discourse.slicer.org/u/Junshi_Peng)\
**Replies:** 1\
**Last updated:** [March 21, 2023, 1:55am UTC](https://discourse.slicer.org/t/can-volumereconstructor-function-run-on-gpu/21257 "2023-03-21T01:55:17Z")

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I’m tring to reconstruct volume from a set of ultrasound images, and I am trying to get the output with less time cost. I have switched the interpolate method into NEAREST\_NEIGHBOR and turn off the hole filling, but it s…

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## [After CT image rotation & flipping by \[Reformat\], how to save? I export reformatted DICOM, but get no change at all](https://discourse.slicer.org/t/after-ct-image-rotation-flipping-by-reformat-how-to-save-i-export-reformatted-dicom-but-get-no-change-at-all/28475)

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**Author:** [@Teddy](https://discourse.slicer.org/u/Teddy)\
**Replies:** 1\
**Last updated:** [March 21, 2023, 1:41am UTC](https://discourse.slicer.org/t/after-ct-image-rotation-flipping-by-reformat-how-to-save-i-export-reformatted-dicom-but-get-no-change-at-all/28475 "2023-03-21T01:41:57Z")

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## [Convert 4d and 3d ultrasounds from Dicom to STL](https://discourse.slicer.org/t/convert-4d-and-3d-ultrasounds-from-dicom-to-stl/28448)

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**Author:** [@Diego.Rlz](https://discourse.slicer.org/u/Diego.Rlz)\
**Replies:** 7\
**Last updated:** [March 20, 2023, 5:38pm UTC](https://discourse.slicer.org/t/convert-4d-and-3d-ultrasounds-from-dicom-to-stl/28448 "2023-03-20T17:38:01Z")

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Operating system: Windows 10 Slicer version: 5.2.2 Expected behavior: I want to load the dicom file from a 4d ultrasound and convert it to .stl Actual behavior: In the 3 view windows just 1 displays an image, the othe…

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## [How to control a running slicer from the command line](https://discourse.slicer.org/t/how-to-control-a-running-slicer-from-the-command-line/28464)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [March 20, 2023, 4:17pm UTC](https://discourse.slicer.org/t/how-to-control-a-running-slicer-from-the-command-line/28464 "2023-03-20T16:17:35Z")

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I know how to use the python console to control slicer. But now I want to control the python console through an external program, My idea is to control the python console by entering commands through cmd, and then cont…

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## [Plastimatch DRR Generation Export](https://discourse.slicer.org/t/plastimatch-drr-generation-export/28455)

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**Author:** [@crissina0905](https://discourse.slicer.org/u/crissina0905)\
**Replies:** 3\
**Last updated:** [March 20, 2023, 3:22pm UTC](https://discourse.slicer.org/t/plastimatch-drr-generation-export/28455 "2023-03-20T15:22:01Z")

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Hi everyone, I am trying to generate 2D digitally reconstructed radiographs from 3D CT scans of the abdomen using the ‘Plastimatch DRR generation’ module. When the DRR renders in the software it looks like the image bel…

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## [Create new line: Fiducial marker to Plane](https://discourse.slicer.org/t/create-new-line-fiducial-marker-to-plane/17572)

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**Author:** [@mcastr](https://discourse.slicer.org/u/mcastr)\
**Replies:** 6\
**Last updated:** [March 20, 2023, 3:05pm UTC](https://discourse.slicer.org/t/create-new-line-fiducial-marker-to-plane/17572 "2023-03-20T15:05:05Z")

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Operating system:Windows 10/ 64 Slicer version:4.11.20200930 Expected behavior:Unk Actual behavior: Is there a way for a line to be projected from a point to a plane at a designated angle? For example on a skull, a pl…

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## [SlicerLookingGlass Extension: Slicer models are stretched and distorted on the Quilt](https://discourse.slicer.org/t/slicerlookingglass-extension-slicer-models-are-stretched-and-distorted-on-the-quilt/28303)

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**Author:** [@mircat](https://discourse.slicer.org/u/mircat)\
**Replies:** 2\
**Last updated:** [March 20, 2023, 2:03pm UTC](https://discourse.slicer.org/t/slicerlookingglass-extension-slicer-models-are-stretched-and-distorted-on-the-quilt/28303 "2023-03-20T14:03:08Z")

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Hello! When generating a quilt using the SlicerLookingGlass Module, the Slicer model becomes stretched, resulting in a blurry and distorted image on the Looking Glass Portrait. See image below. I have a cube model which…

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## [Measurement of density](https://discourse.slicer.org/t/measurement-of-density/28473)

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**Author:** [@choudhurydinesh](https://discourse.slicer.org/u/choudhurydinesh)\
**Replies:** 0\
**Last updated:** [March 20, 2023, 1:49pm UTC](https://discourse.slicer.org/t/measurement-of-density/28473 "2023-03-20T13:49:20Z")

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Hi… Is it possible to determine the density of samples qualitatively using colour gradient? That colour intensity can be used for comparing density between samples. Thank you…

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## [Extract centeline Auto-detect tree mode](https://discourse.slicer.org/t/extract-centeline-auto-detect-tree-mode/26576)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 10\
**Last updated:** [March 20, 2023, 1:19pm UTC](https://discourse.slicer.org/t/extract-centeline-auto-detect-tree-mode/26576 "2023-03-20T13:19:07Z")

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Hello, I am using the Extact Centerline module with Endpoints Autodetect to generate the centerlines over all the vessels of a coronary tree. For this I use the tree option. After a couple of attempts and smoothing the…

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## [Encoding Error for DICOM File from Chison](https://discourse.slicer.org/t/encoding-error-for-dicom-file-from-chison/28437)

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**Author:** [@HMAH](https://discourse.slicer.org/u/HMAH)\
**Replies:** 6\
**Last updated:** [March 20, 2023, 4:53am UTC](https://discourse.slicer.org/t/encoding-error-for-dicom-file-from-chison/28437 "2023-03-20T04:53:47Z")

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Hi everyone, It’s my first time using 3D Slicer and I hit a big road block at my very first step which is importing the DICOM file to the software. The software show me a number of faults which are: DICOM dataset co…

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## [Rescale .stl file based on CT image series info](https://discourse.slicer.org/t/rescale-stl-file-based-on-ct-image-series-info/28459)

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**Author:** [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Replies:** 4\
**Last updated:** [March 19, 2023, 9:41pm UTC](https://discourse.slicer.org/t/rescale-stl-file-based-on-ct-image-series-info/28459 "2023-03-19T21:41:13Z")

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Hello everyone, I would like to ask how to rescale a .stl file, when I only have information on the pixel spacing of the CT image series. I acquired .stl file from MorphoSource, where they also have the CT image series …

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## [Intensity threshold inversion](https://discourse.slicer.org/t/intensity-threshold-inversion/28440)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [March 19, 2023, 8:19pm UTC](https://discourse.slicer.org/t/intensity-threshold-inversion/28440 "2023-03-19T20:19:01Z")

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it would be great if intensity threshold inversion is possible. In some instances, you need a threshold that’s not continuous. so you can pick the intensity you don’t want on histogram and segment the rest ABOVE AND BE…

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## [Orienting .tiff images in axial/sagittal planes](https://discourse.slicer.org/t/orienting-tiff-images-in-axial-sagittal-planes/28456)

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**Author:** [@Liza\_Harold](https://discourse.slicer.org/u/Liza_Harold)\
**Replies:** 1\
**Last updated:** [March 19, 2023, 7:17pm UTC](https://discourse.slicer.org/t/orienting-tiff-images-in-axial-sagittal-planes/28456 "2023-03-19T19:17:22Z")

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I have two stacks of .png images, imported as .tiff files, corresponding to axial and sagittal MRI data. Once I put them into Slicer using the “Data” panel, both stacks are only visible using the “Axial” view. I am tryin…

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## [ROI cropping and segmentation](https://discourse.slicer.org/t/roi-cropping-and-segmentation/28434)

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**Author:** [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Replies:** 1\
**Last updated:** [March 18, 2023, 8:11pm UTC](https://discourse.slicer.org/t/roi-cropping-and-segmentation/28434 "2023-03-18T20:11:31Z")

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Hi, In case of feature extraction from ct images and for any analysis such as prediction, should we crop then segment ROI or just segmentation is enough? Prof @lassoan,@rbumm I would appreciate if you share your opinio…

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## [Combination segmentation effect](https://discourse.slicer.org/t/combination-segmentation-effect/27632)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 8\
**Last updated:** [March 18, 2023, 6:28pm UTC](https://discourse.slicer.org/t/combination-segmentation-effect/27632 "2023-03-18T18:28:55Z")

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i wish that we could have a combination of effect tools the following is what I would love to use 1 combined erase/ median smooth 2 combined paint / median smooth. those would be great time savers instead of applying…

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## [Not reading the binary image](https://discourse.slicer.org/t/not-reading-the-binary-image/28445)

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**Author:** [@moh.askarzade](https://discourse.slicer.org/u/moh.askarzade)\
**Replies:** 0\
**Last updated:** [March 18, 2023, 6:16pm UTC](https://discourse.slicer.org/t/not-reading-the-binary-image/28445 "2023-03-18T18:16:26Z")

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Why don’t SegmentationAidedRegistration or Distance Map Based Registration modules import masks in the form of value or segment in fixed or moving mask? What is the problem and the solution?

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## [Fail to Run Total Segmentator](https://discourse.slicer.org/t/fail-to-run-total-segmentator/28436)

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**Author:** [@holo031029](https://discourse.slicer.org/u/holo031029)\
**Replies:** 1\
**Last updated:** [March 18, 2023, 4:30pm UTC](https://discourse.slicer.org/t/fail-to-run-total-segmentator/28436 "2023-03-18T16:30:24Z")

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Version 5.3 and 5.2.2 both have the same error： Updated the Total Segmentator package and error in the first time, then RUN it again the processing started but still can’t work successfully. Thanks for your help! Tra…

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## [LungCTAnalyzer input file error](https://discourse.slicer.org/t/lungctanalyzer-input-file-error/28301)

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**Author:** [@JasonYangchen](https://discourse.slicer.org/u/JasonYangchen)\
**Replies:** 19\
**Last updated:** [March 18, 2023, 9:34am UTC](https://discourse.slicer.org/t/lungctanalyzer-input-file-error/28301 "2023-03-18T09:34:49Z")

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CUDA available: True 3Dslicer5.0.3 Error occurs when I use my patient data RuntimeError: unexpected EOF, expected 10008318 more bytes. The file might be corrupted. How con I slove this problem? thanks

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## [CT image filtering/preprocessing](https://discourse.slicer.org/t/ct-image-filtering-preprocessing/28427)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 0\
**Last updated:** [March 17, 2023, 1:34pm UTC](https://discourse.slicer.org/t/ct-image-filtering-preprocessing/28427 "2023-03-17T13:34:58Z")

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Hi all, I am working with heart CT images. Sometimes the quality is low and vessel walls are blurred. Commercial software is capable of preprocess images to obtain results such as: I tried a combination of filters i…

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## [Trouble with Extension "SurfaceWrapSolidify" ](https://discourse.slicer.org/t/trouble-with-extension-surfacewrapsolidify/28331)

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**Author:** [@German.Men.Rev](https://discourse.slicer.org/u/German.Men.Rev)\
**Replies:** 6\
**Last updated:** [March 17, 2023, 12:48pm UTC](https://discourse.slicer.org/t/trouble-with-extension-surfacewrapsolidify/28331 "2023-03-17T12:48:58Z")

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Hi everybody :grinning: , first time here on this forum. Hope I chose the right category. I was having some trouble with the Extension “SurfaceWrapSolidify” . It’s a pelvic CT with a superior pubic ramus fracture , and …

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## [What does the indicator mean in the final output result of LungCTAnalyzer](https://discourse.slicer.org/t/what-does-the-indicator-mean-in-the-final-output-result-of-lungctanalyzer/28422)

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**Author:** [@zhenhua3](https://discourse.slicer.org/u/zhenhua3)\
**Replies:** 3\
**Last updated:** [March 17, 2023, 10:41am UTC](https://discourse.slicer.org/t/what-does-the-indicator-mean-in-the-final-output-result-of-lungctanalyzer/28422 "2023-03-17T10:41:08Z")

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Dear Professor Rudolf Bumm hay，I’m trying to use the LungCTAnalyzer Tool to calculate lung volume,But I don’t understand the result output by the LungCTAnalyzer.Such as:Emphysema right;Inflated right ;Infiltration right…

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## [Edit existing segments without the original volume](https://discourse.slicer.org/t/edit-existing-segments-without-the-original-volume/28253)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 2\
**Last updated:** [March 17, 2023, 10:08am UTC](https://discourse.slicer.org/t/edit-existing-segments-without-the-original-volume/28253 "2023-03-17T10:08:52Z")

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Hi Have few segmented bones which are not correctly segmented. The outline has holes. I would like to correct them by solidifying them, correcting the outline. However I do not have the original 3D CT volume for these. I…

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## [I try to use asyncio rather than qt.QTcpSocket as the client, but the socket can receive msgs only if the mouse is hovering the the Slicer UI](https://discourse.slicer.org/t/i-try-to-use-asyncio-rather-than-qt-qtcpsocket-as-the-client-but-the-socket-can-receive-msgs-only-if-the-mouse-is-hovering-the-the-slicer-ui/28411)

<div class="topic-metadata">

**Author:** [@derekcbr](https://discourse.slicer.org/u/derekcbr)\
**Replies:** 4\
**Last updated:** [March 17, 2023, 1:02am UTC](https://discourse.slicer.org/t/i-try-to-use-asyncio-rather-than-qt-qtcpsocket-as-the-client-but-the-socket-can-receive-msgs-only-if-the-mouse-is-hovering-the-the-slicer-ui/28411 "2023-03-17T01:02:13Z")

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import asyncio async def tcp\_echo\_client(message): reader, writer = await asyncio.open\_connection( '127.0.0.1', 8888) print(f'Send: {message!r}') writer.write(message.encode()) await writer.drai…

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## [Qt5\_DIR-NOTFOUND](https://discourse.slicer.org/t/qt5-dir-notfound/28402)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 2\
**Last updated:** [March 16, 2023, 4:33pm UTC](https://discourse.slicer.org/t/qt5-dir-notfound/28402 "2023-03-16T16:33:13Z")

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Hello everyone, I’m trying to configure 3D Slicer in ubuntu using ccmake … I installed Qt5, but still it can’t find some directories as shown in the below screenshot Would you mind suggesting how I can possibly sol…

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