# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=411

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

**Page:** 412

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## [Sequences module](https://discourse.slicer.org/t/sequences-module/4210)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 0\
**Last updated:** [September 27, 2018, 2:58pm UTC](https://discourse.slicer.org/t/sequences-module/4210 "2018-09-27T14:58:00Z")

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HI Could someone kindly let me know why I cannot build up a new sequence from combining previously loaded 2 sequences please. I followed the steps on sequences document, but sequence browser does not play back the combin…

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## [Generating STL volumes from DICOM data](https://discourse.slicer.org/t/generating-stl-volumes-from-dicom-data/4181)

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**Author:** [@Deyline](https://discourse.slicer.org/u/Deyline)\
**Replies:** 4\
**Last updated:** [September 27, 2018, 11:14am UTC](https://discourse.slicer.org/t/generating-stl-volumes-from-dicom-data/4181 "2018-09-27T11:14:02Z")

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Hello Slicer wizards, I’ve been using Slicer for the past days and I’ve been having some problems with generating volumes from the DICOM data that I have. I’ve been mainly following tutorials on youtube, but I can’t see…

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## [Problem using VMTK](https://discourse.slicer.org/t/problem-using-vmtk/4199)

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**Author:** [@NinoNobile](https://discourse.slicer.org/u/NinoNobile)\
**Replies:** 1\
**Last updated:** [September 27, 2018, 4:58am UTC](https://discourse.slicer.org/t/problem-using-vmtk/4199 "2018-09-27T04:58:19Z")

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Operating system: Windows 10 Slicer version: 4.9.0 Expected behavior: Actual behavior: Hello everyone, I’m trying to use VMTK to create a model of some blood vessel from an MRI study but even though I’ve seen and te…

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## [Combine two DICOM images](https://discourse.slicer.org/t/combine-two-dicom-images/4194)

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**Author:** [@M\_pavi](https://discourse.slicer.org/u/M_pavi)\
**Replies:** 1\
**Last updated:** [September 26, 2018, 8:10pm UTC](https://discourse.slicer.org/t/combine-two-dicom-images/4194 "2018-09-26T20:10:35Z")

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I want to combine two DICOM image together for an example head and neck likewise

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## [Why does the shape of the image change?](https://discourse.slicer.org/t/why-does-the-shape-of-the-image-change/4192)

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**Author:** [@zgk110](https://discourse.slicer.org/u/zgk110)\
**Replies:** 1\
**Last updated:** [September 26, 2018, 2:23pm UTC](https://discourse.slicer.org/t/why-does-the-shape-of-the-image-change/4192 "2018-09-26T14:23:12Z")

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Hi, I read a MRI series image by Simpleitk and the shape of it is (168L, 640L, 640L). However, when i use the 3D slicer to read the same image, the shape of the image is changed to (24L, 640L, 640L), meanwhile, I find t…

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## [Creation of a new module which contains a transparent adjustable overlay](https://discourse.slicer.org/t/creation-of-a-new-module-which-contains-a-transparent-adjustable-overlay/4183)

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**Author:** [@katharina\_hecker](https://discourse.slicer.org/u/katharina_hecker)\
**Replies:** 7\
**Last updated:** [September 26, 2018, 11:47am UTC](https://discourse.slicer.org/t/creation-of-a-new-module-which-contains-a-transparent-adjustable-overlay/4183 "2018-09-26T11:47:46Z")

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Hi everyone, I was wondering if it is possible to create a new module, which can load in the coronal window an transparent overlay, which is adjustable (stretchable…). This overlay consists of several images which you …

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## [Matlab transform issue](https://discourse.slicer.org/t/matlab-transform-issue/2276)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [September 25, 2018, 7:59pm UTC](https://discourse.slicer.org/t/matlab-transform-issue/2276 "2018-09-25T19:59:55Z")

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I am quite confused. I have a .mat that I want to apply bunch of points. Slicer does it correctly. This is the transform that it displays in the Information tab: Transform to parent: 0.999281 0.0298646 -0.0233499 -9.08…

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## [Regarding .h5 file format](https://discourse.slicer.org/t/regarding-h5-file-format/4172)

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**Author:** [@jamieng](https://discourse.slicer.org/u/jamieng)\
**Replies:** 5\
**Last updated:** [September 25, 2018, 4:43pm UTC](https://discourse.slicer.org/t/regarding-h5-file-format/4172 "2018-09-25T16:43:56Z")

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Hello, May I know if .h5 file formats are editable in 3D Slicer to perform segmentation? If it is not, may I know if it is possible to easily convert the file to a compatible and editable format in 3D Slicer? Thank yo…

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## [volumetric analysis of mouse brain structures ](https://discourse.slicer.org/t/volumetric-analysis-of-mouse-brain-structures/4180)

<div class="topic-metadata">

**Author:** [@jsramos](https://discourse.slicer.org/u/jsramos)\
**Replies:** 2\
**Last updated:** [September 25, 2018, 3:03am UTC](https://discourse.slicer.org/t/volumetric-analysis-of-mouse-brain-structures/4180 "2018-09-25T03:03:06Z")

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Using MR T1 weighted images in DICOM format, I am not sure how to manually designate the anatomical structures of interest and to calculate volumes of these structures as well as the signal density within these struct…

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## [Issues during TBI segmentation using ABC](https://discourse.slicer.org/t/issues-during-tbi-segmentation-using-abc/4159)

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**Author:** [@Alexxx9596](https://discourse.slicer.org/u/Alexxx9596)\
**Replies:** 3\
**Last updated:** [September 24, 2018, 7:03pm UTC](https://discourse.slicer.org/t/issues-during-tbi-segmentation-using-abc/4159 "2018-09-24T19:03:50Z")

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Hello Slicer community! First post on a public forum so bare with me. I am attempting to segment brain lesions using Atlas based classification (ABC). Following through the tutorials that are provided both on this webpa…

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## [Read Prostate MR image failed](https://discourse.slicer.org/t/read-prostate-mr-image-failed/3423)

<div class="topic-metadata">

**Author:** [@zgk110](https://discourse.slicer.org/u/zgk110)\
**Replies:** 9\
**Last updated:** [September 23, 2018, 12:54pm UTC](https://discourse.slicer.org/t/read-prostate-mr-image-failed/3423 "2018-09-23T12:54:21Z")

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Operating system:Windows 64 bit Slicer version:4.8.1 Expected behavior: Actual behavior: Hello, i am trying to read a prostate image by 3D slicer, however, when i open it, it seems some of the images is not com…

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## [Track motion of anatomical points in 4D DICOM image](https://discourse.slicer.org/t/track-motion-of-anatomical-points-in-4d-dicom-image/4169)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 6\
**Last updated:** [September 23, 2018, 3:19am UTC](https://discourse.slicer.org/t/track-motion-of-anatomical-points-in-4d-dicom-image/4169 "2018-09-23T03:19:31Z")

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Operating system: Windows 10 Slicer version:4.9 Expected behavior: Actual behavior: Could someone kindly advise on how to analyse 4 D dicom data using slicer please. I can not even get it to load to slicer (one serie…

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## [Build only selected extensions](https://discourse.slicer.org/t/build-only-selected-extensions/4158)

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**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\
**Replies:** 2\
**Last updated:** [September 20, 2018, 6:30pm UTC](https://discourse.slicer.org/t/build-only-selected-extensions/4158 "2018-09-20T18:30:34Z")

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Hi! I’m building Slicer Git Master myself, and therefore also the Extensions. However, since it takes a long time, I would like to only build a few selected extensions. Is there a more elegant way of doing it than delet…

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## [Surface details in segmenting](https://discourse.slicer.org/t/surface-details-in-segmenting/4154)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 11\
**Last updated:** [September 20, 2018, 3:05pm UTC](https://discourse.slicer.org/t/surface-details-in-segmenting/4154 "2018-09-20T15:05:18Z")

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I am new to slicer. I tried segmenting small bones from 3D DICOM images and the 3 d image quality is not very clear as shown in videos. Like bone surface are not smooth ( if I make it smooth by surface tools module, I lo…

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## [Curved 3D MPR from input coordinates](https://discourse.slicer.org/t/curved-3d-mpr-from-input-coordinates/4080)

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**Author:** [@LineM](https://discourse.slicer.org/u/LineM)\
**Replies:** 7\
**Last updated:** [September 20, 2018, 3:03pm UTC](https://discourse.slicer.org/t/curved-3d-mpr-from-input-coordinates/4080 "2018-09-20T15:03:34Z")

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Operating system: Windows Slicer version: 4.8.1 I’ve tried to find an answer to this question on the wiki pages, but haven’t been able to find it: Is it possible to use Slicer to generate a curved 3D multiplanar recon…

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## [Dual energy series reconstruction](https://discourse.slicer.org/t/dual-energy-series-reconstruction/4136)

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**Author:** [@opetne](https://discourse.slicer.org/u/opetne)\
**Replies:** 2\
**Last updated:** [September 20, 2018, 12:41pm UTC](https://discourse.slicer.org/t/dual-energy-series-reconstruction/4136 "2018-09-20T12:41:06Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: Hi folks! I have a series of dog contrast head CT, made on Siemens Definition Flash with dual energy. I’d like to reconstruct the vasculature onl…

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## [Intrasubject Breast pre- and post-treatment MRI registration](https://discourse.slicer.org/t/intrasubject-breast-pre-and-post-treatment-mri-registration/4153)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 1\
**Last updated:** [September 20, 2018, 3:48am UTC](https://discourse.slicer.org/t/intrasubject-breast-pre-and-post-treatment-mri-registration/4153 "2018-09-20T03:48:49Z")

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Hi everyone, I have some questions about Slicer Registration Library Case #6: Breast MRI Cancer Treatment. (https://www.slicer.org/wiki/Documentation:Nightly:Registration:RegistrationLibrary:RegLib\_C06 Does the mask r…

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## [Calculating Relative CT Perfusion](https://discourse.slicer.org/t/calculating-relative-ct-perfusion/633)

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**Author:** [@hph10128](https://discourse.slicer.org/u/hph10128)\
**Replies:** 3\
**Last updated:** [September 18, 2018, 7:15pm UTC](https://discourse.slicer.org/t/calculating-relative-ct-perfusion/633 "2018-09-18T19:15:05Z")

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Hi! I was wondering if there were any modules or extensions that could do a relative perfusion CT calculation. I have an absolute perfusion CBF and CBV and want to calculate relative CBF and CBVs. If not, if any one ha…

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## [Intersection two models (Plane and centerlines CT/MR)](https://discourse.slicer.org/t/intersection-two-models-plane-and-centerlines-ct-mr/4130)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 2\
**Last updated:** [September 18, 2018, 9:01am UTC](https://discourse.slicer.org/t/intersection-two-models-plane-and-centerlines-ct-mr/4130 "2018-09-18T09:01:32Z")

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Hi 3DSlicer users and developers I’m sorry that I repeat my question in another way. I still have problem to find the points of collision. As you can see, I have three models. Model 1 (CenterlinesMRI): Model 2 (Ce…

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## [Convert model to landmarks](https://discourse.slicer.org/t/convert-model-to-landmarks/4139)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 1\
**Last updated:** [September 18, 2018, 12:59pm UTC](https://discourse.slicer.org/t/convert-model-to-landmarks/4139 "2018-09-18T12:59:04Z")

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Hi Dear developers and users. With Steve’s tips and guidance, at now I can extract intersection points between lines (centerlinesMR and centerlinesCT) and the plane with model type separately(with python script). In t…

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## [How to convert to .stl from .nii](https://discourse.slicer.org/t/how-to-convert-to-stl-from-nii/4088)

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**Author:** [@xwang2](https://discourse.slicer.org/u/xwang2)\
**Replies:** 2\
**Last updated:** [September 17, 2018, 7:30pm UTC](https://discourse.slicer.org/t/how-to-convert-to-stl-from-nii/4088 "2018-09-17T19:30:04Z")

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Hi everyone, I want to convert this .nii file directly into .stl file which can be used by Netgen, how can I do it without any segmentation in 3DSlicer? Because this file .nii was already a segmentation from itksnap. T…

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## [How to use OpenIGTlinkIF connect RealSense D435 to slicer?](https://discourse.slicer.org/t/how-to-use-openigtlinkif-connect-realsense-d435-to-slicer/4126)

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**Author:** [@TecNerd](https://discourse.slicer.org/u/TecNerd)\
**Replies:** 2\
**Last updated:** [September 17, 2018, 1:35am UTC](https://discourse.slicer.org/t/how-to-use-openigtlinkif-connect-realsense-d435-to-slicer/4126 "2018-09-17T01:35:08Z")

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A video demo posted by PerkLab on YouTube about connecting slicer to the Intel RealSense cameras to receive registered optical image: I googled tutorials, but most tutorials are about tracking system, nothing help. …

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## [How to import dicom series directory by python scripting?](https://discourse.slicer.org/t/how-to-import-dicom-series-directory-by-python-scripting/4124)

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**Author:** [@zgk110](https://discourse.slicer.org/u/zgk110)\
**Replies:** 0\
**Last updated:** [September 16, 2018, 3:40am UTC](https://discourse.slicer.org/t/how-to-import-dicom-series-directory-by-python-scripting/4124 "2018-09-16T03:40:00Z")

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Hi, i am trying to import a dicom series directory by python scripting, i just found the command 'slicer.util.loadNodeFromFile /loadScene/loadVolume ’ , is there any other function to load the dicom series from directory…

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## [How create new GUI module in 3DSlicer?](https://discourse.slicer.org/t/how-create-new-gui-module-in-3dslicer/4118)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 8\
**Last updated:** [September 15, 2018, 7:30am UTC](https://discourse.slicer.org/t/how-create-new-gui-module-in-3dslicer/4118 "2018-09-15T07:30:49Z")

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Hi dear users and developers. How can I create new module for 3DSlicer? I want create new module that is accessible for 3DSlicer users. This module can used in the radiotherapy research. Plastimatch is used in this mod…

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## [Installing non-matching extension from file - better error message is needed](https://discourse.slicer.org/t/installing-non-matching-extension-from-file-better-error-message-is-needed/4121)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [September 14, 2018, 8:31pm UTC](https://discourse.slicer.org/t/installing-non-matching-extension-from-file-better-error-message-is-needed/4121 "2018-09-14T20:31:21Z")

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I was testing installation of extensions from files. When I by mistake tried to install extension package that did not have a matching revision number, I was getting a cryptic error (screenshot below). It would be much m…

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## [error in show 3D function of segment editor module of slicer 4.8.1  ](https://discourse.slicer.org/t/error-in-show-3d-function-of-segment-editor-module-of-slicer-4-8-1/4062)

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**Author:** [@Anis](https://discourse.slicer.org/u/Anis)\
**Replies:** 6\
**Last updated:** [September 14, 2018, 3:22pm UTC](https://discourse.slicer.org/t/error-in-show-3d-function-of-segment-editor-module-of-slicer-4-8-1/4062 "2018-09-14T15:22:45Z")

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I have Ct data of human tooth. I am trying to create stl file for gmesh.I have constructed nrrd using a stack of 300 tomography slices using Fiji. The nrrd file is 9.2MB. I could segment the data but show 3D doesn’t work…

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## [No extensions in extension manager](https://discourse.slicer.org/t/no-extensions-in-extension-manager/4117)

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**Author:** [@vincitytaymodaimo](https://discourse.slicer.org/u/vincitytaymodaimo)\
**Replies:** 1\
**Last updated:** [September 14, 2018, 1:14pm UTC](https://discourse.slicer.org/t/no-extensions-in-extension-manager/4117 "2018-09-14T13:14:58Z")

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Hi! After installing Slicer 4.9.0 2018-08-07, there are no extensions listed in the extension manager. In the extensions manager, I get the message: “No extensions found for win:64-bit, revision: ‘27339’. Please try a d…

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## [Want to use , slicer which is installed on cloud virtual machine](https://discourse.slicer.org/t/want-to-use-slicer-which-is-installed-on-cloud-virtual-machine/4116)

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**Author:** [@anandmulay3](https://discourse.slicer.org/u/anandmulay3)\
**Replies:** 2\
**Last updated:** [September 14, 2018, 12:20pm UTC](https://discourse.slicer.org/t/want-to-use-slicer-which-is-installed-on-cloud-virtual-machine/4116 "2018-09-14T12:20:06Z")

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Hi , I’m trying to use slicer on cloud virtual machine, i tried to use Nomachine, team viewer, and real Vnc, please suggest me a rdp client or if i’m missing any settings in these software’s. Thanks

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## [Deformable Registration Grid DICOM import](https://discourse.slicer.org/t/deformable-registration-grid-dicom-import/4095)

<div class="topic-metadata">

**Author:** [@Lowey](https://discourse.slicer.org/u/Lowey)\
**Replies:** 1\
**Last updated:** [September 13, 2018, 4:57am UTC](https://discourse.slicer.org/t/deformable-registration-grid-dicom-import/4095 "2018-09-13T04:57:38Z")

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Hi there, I am trying to get my head around how Slicer reads TPS exported Displacement fields and calculates its Grid Orientation values. For example, I have exported an arbitrary displacement field from my TPS and hav…

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## [Broken .mrb file after saving fiducial list with "&" character in title](https://discourse.slicer.org/t/broken-mrb-file-after-saving-fiducial-list-with-character-in-title/4110)

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**Author:** [@mfolson](https://discourse.slicer.org/u/mfolson)\
**Replies:** 1\
**Last updated:** [September 13, 2018, 9:06pm UTC](https://discourse.slicer.org/t/broken-mrb-file-after-saving-fiducial-list-with-character-in-title/4110 "2018-09-13T21:06:17Z")

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Running Slicer 4.8.1 on Windows 7. Created a new fiducial list with “&” in the title and saved as .mrb file. I can keep working on the file without issue as long as it is not closed. When trying to reopen the .mrb, all …

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