# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=227

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

**Page:** 228

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## [Rigid landmark registration for models](https://discourse.slicer.org/t/rigid-landmark-registration-for-models/23075)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 1\
**Last updated:** [April 23, 2022, 5:04am UTC](https://discourse.slicer.org/t/rigid-landmark-registration-for-models/23075 "2022-04-23T05:04:28Z")

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I forget, is there a module for using landmarks to rigidly align models and images together in 3D space? I am hoping to be able to do principal component analysis from the SLicerMorph module while retaining the size dime…

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## [Any Log4J vulnerabilities (Apache Java)  ](https://discourse.slicer.org/t/any-log4j-vulnerabilities-apache-java/23087)

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**Author:** [@car](https://discourse.slicer.org/u/car)\
**Replies:** 3\
**Last updated:** [April 23, 2022, 4:40am UTC](https://discourse.slicer.org/t/any-log4j-vulnerabilities-apache-java/23087 "2022-04-23T04:40:31Z")

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Hi, apologies if this is a daft question, but I need to confirm that there are no Log4J vulnerabilities associated with 3D Slicer please. I don’t use it personally, but it is used within our organisation and I am tasked…

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## [Segment Geometry error](https://discourse.slicer.org/t/segment-geometry-error/21060)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 6\
**Last updated:** [April 23, 2022, 3:35am UTC](https://discourse.slicer.org/t/segment-geometry-error/21060 "2022-04-23T03:35:50Z")

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Hello~everyone~ I had a problem while using the segment geometry module. The module would work sometimes, but it will not work most of the time and show me an error message as below… Slicer has caught an application e…

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## [Question about applying automatic maximum entropy on the FDG PET image](https://discourse.slicer.org/t/question-about-applying-automatic-maximum-entropy-on-the-fdg-pet-image/23048)

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**Author:** [@Jinny\_Lee](https://discourse.slicer.org/u/Jinny_Lee)\
**Replies:** 3\
**Last updated:** [April 21, 2022, 10:32am UTC](https://discourse.slicer.org/t/question-about-applying-automatic-maximum-entropy-on-the-fdg-pet-image/23048 "2022-04-21T10:32:14Z")

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Hi, I’m currently working on FDG PET images to segment a tumor using automatic maximum entropy. I thought the maximum entropy would be able to automatically segment the tumor, but it selects other organs like the heart …

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## [Bug: zoom in linked slices gets out of sync when using right-click+drag (again)](https://discourse.slicer.org/t/bug-zoom-in-linked-slices-gets-out-of-sync-when-using-right-click-drag-again/22996)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 5\
**Last updated:** [April 21, 2022, 1:20am UTC](https://discourse.slicer.org/t/bug-zoom-in-linked-slices-gets-out-of-sync-when-using-right-click-drag-again/22996 "2022-04-21T01:20:00Z")

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I linked the slice views and when I right-click+drag to change the field of view (zoom), only the field of view of the slice where my mouse is is changed. When I use ctrl+scroll all the linked slice views are synchronis…

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## [Error when using reduced nrrd file](https://discourse.slicer.org/t/error-when-using-reduced-nrrd-file/23062)

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**Author:** [@ekt](https://discourse.slicer.org/u/ekt)\
**Replies:** 1\
**Last updated:** [April 21, 2022, 12:19am UTC](https://discourse.slicer.org/t/error-when-using-reduced-nrrd-file/23062 "2022-04-21T00:19:43Z")

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I had a very large file (~4.4GB) so I used Fiji to reduce the number of images and bring the file size down to 1.5GB. Now when I try to load it into slicer the images don’t seem to have any width? They all show up in the…

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## [Stack Align images before segmentation](https://discourse.slicer.org/t/stack-align-images-before-segmentation/23060)

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**Author:** [@bhowmisp](https://discourse.slicer.org/u/bhowmisp)\
**Replies:** 0\
**Last updated:** [April 20, 2022, 8:37pm UTC](https://discourse.slicer.org/t/stack-align-images-before-segmentation/23060 "2022-04-20T20:37:29Z")

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Hi, I have axial cryosection image dataset which are incorrectly aligned leading to somewhat improper segmentations. Is there any plugin available to properly stack align these, before I segment them? Attached is the s…

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## [How to annotate Bronchopulmonary segments in CT on 3D Slicer ?](https://discourse.slicer.org/t/how-to-annotate-bronchopulmonary-segments-in-ct-on-3d-slicer/23046)

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**Author:** [@Joris\_Fournel](https://discourse.slicer.org/u/Joris_Fournel)\
**Replies:** 4\
**Last updated:** [April 20, 2022, 8:33pm UTC](https://discourse.slicer.org/t/how-to-annotate-bronchopulmonary-segments-in-ct-on-3d-slicer/23046 "2022-04-20T20:33:14Z")

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Hello to all the community here, Me and my research team are currently hitting a wall in trying to identify a process in 3D slicer to annotate Bronchopulmonary segments in CT with 3D Slicer. Which brings me on this for…

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## [New user: Loading non-dicom data](https://discourse.slicer.org/t/new-user-loading-non-dicom-data/23054)

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**Author:** [@CamRiddle22](https://discourse.slicer.org/u/CamRiddle22)\
**Replies:** 7\
**Last updated:** [April 20, 2022, 7:03pm UTC](https://discourse.slicer.org/t/new-user-loading-non-dicom-data/23054 "2022-04-20T19:03:19Z")

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Hi Slicer community. I am an undergraduate student assisting in research and I am brand new to 3D modeling. Our research involves scans of fish and we have 10 or so folders with the scan data. The only downside that I ha…

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## [Question about calibration](https://discourse.slicer.org/t/question-about-calibration/23035)

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**Author:** [@user5](https://discourse.slicer.org/u/user5)\
**Replies:** 1\
**Last updated:** [April 20, 2022, 4:17pm UTC](https://discourse.slicer.org/t/question-about-calibration/23035 "2022-04-20T16:17:56Z")

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Hello everyone. I am trying yo use ArUco Marker to be the tracker to perform a Brain surgery navigation test. I have followed every step in tutorial , the needle still go to wrong location. I already retry it for many t…

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## [SlicerANTs in 3DSlicer](https://discourse.slicer.org/t/slicerants-in-3dslicer/23038)

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**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 2\
**Last updated:** [April 20, 2022, 2:26pm UTC](https://discourse.slicer.org/t/slicerants-in-3dslicer/23038 "2022-04-20T14:26:34Z")

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Dear All, I have not found the SlicerANTs extension in the extension manager (I use Slicer 4.11 version), Furthermore, when I install it via GitHub I cannot find it anywhere among extensions. Do you have any idea how t…

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## [Normalise segmentations to MNI space](https://discourse.slicer.org/t/normalise-segmentations-to-mni-space/23045)

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**Author:** [@Hamoun\_Rozati](https://discourse.slicer.org/u/Hamoun_Rozati)\
**Replies:** 1\
**Last updated:** [April 20, 2022, 12:23pm UTC](https://discourse.slicer.org/t/normalise-segmentations-to-mni-space/23045 "2022-04-20T12:23:16Z")

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Hello all. I have a couple hundred MRI scans of patients with brain metastases which have been segmented. I want to create a heat map of all the lesions. I can normalise the individual MRI scans to MNI space using SPM12,…

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## [Tracking changes in the lung CT](https://discourse.slicer.org/t/tracking-changes-in-the-lung-ct/23016)

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**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 3\
**Last updated:** [April 20, 2022, 12:02pm UTC](https://discourse.slicer.org/t/tracking-changes-in-the-lung-ct/23016 "2022-04-20T12:02:46Z")

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Dear all, I am currently working on lung CT to evaluate the changes in lung tissue and tumor size. I have CT scans at 8 different time points such as Planning CT, Therapy Control CT, and Follow-up CTs. I want to use pl…

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## [transversal DICOM image distorted and coronal DICOM image well](https://discourse.slicer.org/t/transversal-dicom-image-distorted-and-coronal-dicom-image-well/12529)

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**Author:** [@MarCollado](https://discourse.slicer.org/u/MarCollado)\
**Replies:** 14\
**Last updated:** [April 20, 2022, 11:27am UTC](https://discourse.slicer.org/t/transversal-dicom-image-distorted-and-coronal-dicom-image-well/12529 "2022-04-20T11:27:39Z")

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Operating system:Windows10 Slicer version:4.10.2 Expected behavior:non distorted images Actual behavior: distorted transversal image and non-distorted coronal image Dear Sir or Madame: I am Mar Collado from the Univ…

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## [Using python to automate pseudoLMGenerator and ALPACA processes](https://discourse.slicer.org/t/using-python-to-automate-pseudolmgenerator-and-alpaca-processes/22851)

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**Author:** [@Erik.Meilak](https://discourse.slicer.org/u/Erik.Meilak)\
**Replies:** 5\
**Last updated:** [April 20, 2022, 10:46am UTC](https://discourse.slicer.org/t/using-python-to-automate-pseudolmgenerator-and-alpaca-processes/22851 "2022-04-20T10:46:57Z")

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Hello, I am trying to automate some processes which use the modules pseudoLMGenerator and ALPACA but cannot find any of the functions which are available in the GUI. For example if I try and set the base mesh in the pse…

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## [Slicer becomes slower over time during surgical navigation cases](https://discourse.slicer.org/t/slicer-becomes-slower-over-time-during-surgical-navigation-cases/20176)

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**Author:** [@Prashant\_Pandey](https://discourse.slicer.org/u/Prashant_Pandey)\
**Replies:** 7\
**Last updated:** [April 20, 2022, 4:04am UTC](https://discourse.slicer.org/t/slicer-becomes-slower-over-time-during-surgical-navigation-cases/20176 "2022-04-20T04:04:09Z")

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We’re using Windows 10, Slicer 4.11, SlicerIGT and PLUS to do navigated surgery. We’re streaming data from an NDI optical tracker and an ultrasound probe using OpenIGTLink. We are running into problems with Slicer slowi…

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## [Grow from seeds creates unwanted regions](https://discourse.slicer.org/t/grow-from-seeds-creates-unwanted-regions/23007)

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**Author:** [@bhowmisp](https://discourse.slicer.org/u/bhowmisp)\
**Replies:** 8\
**Last updated:** [April 19, 2022, 8:11pm UTC](https://discourse.slicer.org/t/grow-from-seeds-creates-unwanted-regions/23007 "2022-04-19T20:11:29Z")

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Hi, I have been using the “grow from seeds” effect to segment the ganglion from the following pictures. I paint in two segments, 1- for the ganglion(yellow)- in all three views across multiple slices and 2. for the back…

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## [Incorrect DICOM import](https://discourse.slicer.org/t/incorrect-dicom-import/23029)

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**Author:** [@Boris33](https://discourse.slicer.org/u/Boris33)\
**Replies:** 0\
**Last updated:** [April 19, 2022, 6:10pm UTC](https://discourse.slicer.org/t/incorrect-dicom-import/23029 "2022-04-19T18:10:33Z")

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Hello, I’m just getting started with 3D Slicer (4.11) and I have problems loading correctly my DICOM volume. The data is acquired from a Siemens CT scanner as IMA files and stacked with a pattern 1.1, 1.2, … 1.200 (1 se…

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## [Creating a volume from 4D Echo](https://discourse.slicer.org/t/creating-a-volume-from-4d-echo/22950)

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**Author:** [@jruben4](https://discourse.slicer.org/u/jruben4)\
**Replies:** 4\
**Last updated:** [April 19, 2022, 5:45pm UTC](https://discourse.slicer.org/t/creating-a-volume-from-4d-echo/22950 "2022-04-19T17:45:51Z")

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I’ve been able to import 4D echo DICOMs, but need a little help with the next step to create a volume render. I’ve gotten to this step, and expected that I would see a volume render in the white box, but I must be missi…

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## [Spectral HU Curve Volume in CT image for grey level mapping](https://discourse.slicer.org/t/spectral-hu-curve-volume-in-ct-image-for-grey-level-mapping/22875)

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**Author:** [@Kailash\_Singh](https://discourse.slicer.org/u/Kailash_Singh)\
**Replies:** 13\
**Last updated:** [April 19, 2022, 9:04am UTC](https://discourse.slicer.org/t/spectral-hu-curve-volume-in-ct-image-for-grey-level-mapping/22875 "2022-04-19T09:04:07Z")

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Spectral HU Curve Volume in CT image for grey level mapping

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## [Anyone needs suggestions on connecting optical navigation and 3D Slicer?](https://discourse.slicer.org/t/anyone-needs-suggestions-on-connecting-optical-navigation-and-3d-slicer/23011)

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**Author:** [@Yeyi](https://discourse.slicer.org/u/Yeyi)\
**Replies:** 0\
**Last updated:** [April 19, 2022, 7:07am UTC](https://discourse.slicer.org/t/anyone-needs-suggestions-on-connecting-optical-navigation-and-3d-slicer/23011 "2022-04-19T07:07:57Z")

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Anyone needs suggestions on connecting optical navigation and 3D Slicer?

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## [Clone From Volume Rendering To Segmentation Editor](https://discourse.slicer.org/t/clone-from-volume-rendering-to-segmentation-editor/23010)

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**Author:** [@e\_hoolahan](https://discourse.slicer.org/u/e_hoolahan)\
**Replies:** 0\
**Last updated:** [April 19, 2022, 7:07am UTC](https://discourse.slicer.org/t/clone-from-volume-rendering-to-segmentation-editor/23010 "2022-04-19T07:07:31Z")

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Greetings! I apologize if this question has been asked previously. I have found that in many cases the quality of the volumes rendered under ‘Volume Rendering’ far surpasses my dismal attempts at creating equivalent se…

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## [Cannot get InceptionV3 to work](https://discourse.slicer.org/t/cannot-get-inceptionv3-to-work/22821)

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**Author:** [@dariodo.fal](https://discourse.slicer.org/u/dariodo.fal)\
**Replies:** 5\
**Last updated:** [April 19, 2022, 12:39am UTC](https://discourse.slicer.org/t/cannot-get-inceptionv3-to-work/22821 "2022-04-19T00:39:41Z")

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Hello, I am currently working with Pytorch through the Slicer 4.13 kernel and I am finding trouble getting the pretrained models to work. My code is the following: from \_\_future\_\_ import print\_function, division import…

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## [Render 3D US Volume with 2D images and tracking data](https://discourse.slicer.org/t/render-3d-us-volume-with-2d-images-and-tracking-data/23002)

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**Author:** [@JJenkins](https://discourse.slicer.org/u/JJenkins)\
**Replies:** 1\
**Last updated:** [April 18, 2022, 9:42pm UTC](https://discourse.slicer.org/t/render-3d-us-volume-with-2d-images-and-tracking-data/23002 "2022-04-18T21:42:08Z")

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Hello, I am looking to use Slicer to generate a 3D ultrasound volume from 2D images and tracking data. The goal is for the image acquisition to be done by hand, so the image spacing will not be regular or in one dimensi…

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## [How to increase the segmentation resolution?](https://discourse.slicer.org/t/how-to-increase-the-segmentation-resolution/22981)

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**Author:** [@Makhlouf](https://discourse.slicer.org/u/Makhlouf)\
**Replies:** 6\
**Last updated:** [April 18, 2022, 9:09pm UTC](https://discourse.slicer.org/t/how-to-increase-the-segmentation-resolution/22981 "2022-04-18T21:09:34Z")

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Hi everybody, How can I increase the resolution of the segmentation as the default one uses large size of voxels (cubes)? Is this called oversampling? how to do it without changing the volume as I need to calculate the…

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## [Create a smooth segmented 3D model from PNG images](https://discourse.slicer.org/t/create-a-smooth-segmented-3d-model-from-png-images/22957)

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**Author:** [@bhowmisp](https://discourse.slicer.org/u/bhowmisp)\
**Replies:** 9\
**Last updated:** [April 18, 2022, 6:49am UTC](https://discourse.slicer.org/t/create-a-smooth-segmented-3d-model-from-png-images/22957 "2022-04-18T06:49:33Z")

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Hi, I have been using the Visible Human project TIFF images to segment out the spinal cord and DRG. The DRG is not clearly visible but I want to get an idea of the relative vertical levels of the DRG and the Spine, espe…

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## [Vessel quantification from micro-CT images](https://discourse.slicer.org/t/vessel-quantification-from-micro-ct-images/22089)

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**Author:** [@Adela\_Garcia](https://discourse.slicer.org/u/Adela_Garcia)\
**Replies:** 3\
**Last updated:** [April 17, 2022, 3:49am UTC](https://discourse.slicer.org/t/vessel-quantification-from-micro-ct-images/22089 "2022-04-17T03:49:28Z")

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Hi, I would like to quantified vascular vessel ( number of vessels, vessel diameter…) in mouse hind limd but first I need to remove the bone.The images to quantified are acquired with micro-CT. Which tools of 3D SLICER a…

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## [Some questions about 3D Slicer](https://discourse.slicer.org/t/some-questions-about-3d-slicer/22982)

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**Author:** [@user\_ghost](https://discourse.slicer.org/u/user_ghost)\
**Replies:** 1\
**Last updated:** [April 16, 2022, 12:35pm UTC](https://discourse.slicer.org/t/some-questions-about-3d-slicer/22982 "2022-04-16T12:35:22Z")

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Hello every teachers: when i opened the 3D Slicer, the software give me a strange message. how can i resolve this problem thanks

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## [3D model showing up as a line?](https://discourse.slicer.org/t/3d-model-showing-up-as-a-line/22955)

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**Author:** [@ekt](https://discourse.slicer.org/u/ekt)\
**Replies:** 4\
**Last updated:** [April 15, 2022, 6:51pm UTC](https://discourse.slicer.org/t/3d-model-showing-up-as-a-line/22955 "2022-04-15T18:51:18Z")

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Operating system: Windows 10 Slicer version: 4.11.2 I am trying to get a volume rendering of my image stack, but it just shows up as a single weird black line (see screenshot)? How do I fix this?

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## [How to extract characteristics of pneumonia?](https://discourse.slicer.org/t/how-to-extract-characteristics-of-pneumonia/22924)

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**Author:** [@wangxiaolan](https://discourse.slicer.org/u/wangxiaolan)\
**Replies:** 4\
**Last updated:** [April 15, 2022, 1:47pm UTC](https://discourse.slicer.org/t/how-to-extract-characteristics-of-pneumonia/22924 "2022-04-15T13:47:02Z")

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Dear teachers, how to extract characteristics of pneumonia。

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