# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=407

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

**Page:** 408

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## [3D surface reconstruction](https://discourse.slicer.org/t/3d-surface-reconstruction/2665)

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**Author:** [@bedolancer](https://discourse.slicer.org/u/bedolancer)\
**Replies:** 4\
**Last updated:** [October 28, 2018, 9:16pm UTC](https://discourse.slicer.org/t/3d-surface-reconstruction/2665 "2018-10-28T21:16:17Z")

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Operating system:mac ,windows Slicer version:4.9 Expected behavior: hello …id like to ask how to get the brain 3d surface reconstruction in slicer with blood vessels in simple way for properative planning thanks al…

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## [Building SLicer 4.10.0 from source on Ubuntu 18.04](https://discourse.slicer.org/t/building-slicer-4-10-0-from-source-on-ubuntu-18-04/4521)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 7\
**Last updated:** [October 28, 2018, 7:07pm UTC](https://discourse.slicer.org/t/building-slicer-4-10-0-from-source-on-ubuntu-18-04/4521 "2018-10-28T19:07:11Z")

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Slicer 4.10.0 with Qt4.8 and VTK 7 is built from source successfully on Ubuntu 18.04 but I had to add this line to the main CMakeList.txt file due to some error related to c11 support. set (CMAKE\_CXX\_STANDARD 11) af…

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## [how to install AutoSeg in Slicer‘s extention](https://discourse.slicer.org/t/how-to-install-autoseg-in-slicer-s-extention/4544)

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**Author:** [@liang23](https://discourse.slicer.org/u/liang23)\
**Replies:** 1\
**Last updated:** [October 28, 2018, 4:39pm UTC](https://discourse.slicer.org/t/how-to-install-autoseg-in-slicer-s-extention/4544 "2018-10-28T16:39:20Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Role the option of “Dose Volume” in the module of “DVH Comparison”?](https://discourse.slicer.org/t/role-the-option-of-dose-volume-in-the-module-of-dvh-comparison/4561)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 1\
**Last updated:** [October 28, 2018, 2:44pm UTC](https://discourse.slicer.org/t/role-the-option-of-dose-volume-in-the-module-of-dvh-comparison/4561 "2018-10-28T14:44:35Z")

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Hi Dear developers and users I have question about “DVH Comparison” module. I can select “DVH 1” and “DVH 2” in the panel of this module, but I do not know the role of “Dose Volume” option in this panel. What is the r…

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## [GEMS\_Ultrasound\_MovieGroup\_001](https://discourse.slicer.org/t/gems-ultrasound-moviegroup-001/1897)

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**Author:** [@Manzoor\_Patel](https://discourse.slicer.org/u/Manzoor_Patel)\
**Replies:** 7\
**Last updated:** [October 28, 2018, 2:08pm UTC](https://discourse.slicer.org/t/gems-ultrasound-moviegroup-001/1897 "2018-10-28T14:08:58Z")

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Operating system: macOS Sierra Slicer version: 4.8.1 Hello Guys, I have a US modality DICOM image which appears to contain the 3D/4D data stored in Spherical or Cylindrical co-ordinates in a private tag (raw-data). Th…

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## [Slicer open .001  .002 files](https://discourse.slicer.org/t/slicer-open-001-002-files/4452)

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**Author:** [@Sukhe](https://discourse.slicer.org/u/Sukhe)\
**Replies:** 21\
**Last updated:** [October 27, 2018, 11:35pm UTC](https://discourse.slicer.org/t/slicer-open-001-002-files/4452 "2018-10-27T23:35:17Z")

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Hi, I am confused by data loading in Slicer. All data I got is ended with .001 .002 .003 etc and I have no idea with the format of those files. I tried in one of my friends Mac and he is using Slicer 4.7.0 which works fo…

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## [Unable to load freesurfer surface in Slicer 4.10 stable and also in 4.11 nightly](https://discourse.slicer.org/t/unable-to-load-freesurfer-surface-in-slicer-4-10-stable-and-also-in-4-11-nightly/4528)

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**Author:** [@devakumar](https://discourse.slicer.org/u/devakumar)\
**Replies:** 8\
**Last updated:** [October 27, 2018, 9:01pm UTC](https://discourse.slicer.org/t/unable-to-load-freesurfer-surface-in-slicer-4-10-stable-and-also-in-4-11-nightly/4528 "2018-10-27T21:01:27Z")

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Dear Slicer team Unable to load freesurfer surface in Slicer 4.10 stable and also in 4.11 nightly. Also, is it possible to load the gii files in 3D Slicer. Regards Devakumar

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## [Volume rendering shows a solid box](https://discourse.slicer.org/t/volume-rendering-shows-a-solid-box/4390)

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**Author:** [@Gary](https://discourse.slicer.org/u/Gary)\
**Replies:** 16\
**Last updated:** [October 27, 2018, 6:04pm UTC](https://discourse.slicer.org/t/volume-rendering-shows-a-solid-box/4390 "2018-10-27T18:04:47Z")

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Hi everyone, As a beginner of this excellent software, Could anyone teach me how to get the surface of the border, which is the line between white and black region?

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## [Radiomics Extension and Butterworth Filter](https://discourse.slicer.org/t/radiomics-extension-and-butterworth-filter/4496)

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**Author:** [@TingtingYu](https://discourse.slicer.org/u/TingtingYu)\
**Replies:** 5\
**Last updated:** [October 25, 2018, 2:48pm UTC](https://discourse.slicer.org/t/radiomics-extension-and-butterworth-filter/4496 "2018-10-25T14:48:47Z")

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Hi, I just download the latest-nightly-built 3D slicer, it turns out that Radiomics seems to be removed from the Extension Manager. May I know why? Another question is I tried to use Butterworth filter with an order of…

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## [Transformations and ras cordinates](https://discourse.slicer.org/t/transformations-and-ras-cordinates/4539)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 0\
**Last updated:** [October 26, 2018, 7:17am UTC](https://discourse.slicer.org/t/transformations-and-ras-cordinates/4539 "2018-10-26T07:17:46Z")

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Hi, I am tracking movement using 4d ct. When I harden the transform in order to copy the RAS coordinates to clip board, I get different reading to not doing so. Eg: My fiducial marker X would give RAS values after trans…

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## [Mix scripting with interaction](https://discourse.slicer.org/t/mix-scripting-with-interaction/4508)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 3\
**Last updated:** [October 26, 2018, 5:36am UTC](https://discourse.slicer.org/t/mix-scripting-with-interaction/4508 "2018-10-26T05:36:54Z")

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I am working on a script that can load matching images and segmentation from levelset. I want to programmatically load each pair, .e.g. case 1, case 2, etc. and then perform edits to the segmentation and then after the …

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## [Access visible widgets](https://discourse.slicer.org/t/access-visible-widgets/4532)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 3\
**Last updated:** [October 26, 2018, 4:09am UTC](https://discourse.slicer.org/t/access-visible-widgets/4532 "2018-10-26T04:09:12Z")

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I know how to grab an active node like this segmentEditorNode = slicer.mrmlScene.GetSingletonNode("SegmentEditor", "vtkMRMLSegmentEditorNode") Is it possible to access the actual widgets without instantiating a new on…

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## [Only one of the 3 views high resolution when importing DICOM files](https://discourse.slicer.org/t/only-one-of-the-3-views-high-resolution-when-importing-dicom-files/4535)

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**Author:** [@SMR](https://discourse.slicer.org/u/SMR)\
**Replies:** 1\
**Last updated:** [October 26, 2018, 3:41am UTC](https://discourse.slicer.org/t/only-one-of-the-3-views-high-resolution-when-importing-dicom-files/4535 "2018-10-26T03:41:34Z")

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Hello, I am having an issue with opening DICOM files. It seems that the data I have is separated out into different series, like T2 coronal and T2 Sag so when I important a file only that specific view is high resolutio…

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## [Any python script can display volume rendering automaticlly after load the DICOM files?](https://discourse.slicer.org/t/any-python-script-can-display-volume-rendering-automaticlly-after-load-the-dicom-files/4527)

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**Author:** [@jiang\_luo](https://discourse.slicer.org/u/jiang_luo)\
**Replies:** 2\
**Last updated:** [October 26, 2018, 3:05am UTC](https://discourse.slicer.org/t/any-python-script-can-display-volume-rendering-automaticlly-after-load-the-dicom-files/4527 "2018-10-26T03:05:45Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: After load the dicom files. the MPR can display automaticlly. but the VR can’t display , any method that can made the VR display automaticlly ??

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## [Open IGT Link for PLUS](https://discourse.slicer.org/t/open-igt-link-for-plus/4529)

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**Author:** [@Felix\_Navarro\_Guirad](https://discourse.slicer.org/u/Felix_Navarro_Guirad)\
**Replies:** 2\
**Last updated:** [October 25, 2018, 5:14pm UTC](https://discourse.slicer.org/t/open-igt-link-for-plus/4529 "2018-10-25T17:14:06Z")

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Dear Slicer users and developers, I’m trying to connect a ultrasound device to Slicer using PLUS server. I’m using Slicer 4.10 and I have installed the IGT and sequeces extensions. I need to install OpenIGTLinkIF but I …

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## [Problem about image are not equally spaced](https://discourse.slicer.org/t/problem-about-image-are-not-equally-spaced/4482)

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**Author:** [@TingtingYu](https://discourse.slicer.org/u/TingtingYu)\
**Replies:** 6\
**Last updated:** [October 25, 2018, 5:46am UTC](https://discourse.slicer.org/t/problem-about-image-are-not-equally-spaced/4482 "2018-10-25T05:46:50Z")

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Hi, I was trying to import patient images, however, I got the warning after I clicked “examine”. Before I loaded the images, I enabled the “DICOMScalarVolumePlugin” as the warning suggested, but the image still appeared…

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## [Segmentation restricted to ROI](https://discourse.slicer.org/t/segmentation-restricted-to-roi/4524)

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**Author:** [@mag](https://discourse.slicer.org/u/mag)\
**Replies:** 1\
**Last updated:** [October 25, 2018, 3:59am UTC](https://discourse.slicer.org/t/segmentation-restricted-to-roi/4524 "2018-10-25T03:59:42Z")

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Hello, this is probably straightforward but after reading through many posts I haven’t been able to figure out how to do it. I am segmenting portions of some vessels on CT angiographies and I want to use “grow from see…

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## [Why is size/shape of numpy array from labelmap and scalar volume not the same?](https://discourse.slicer.org/t/why-is-size-shape-of-numpy-array-from-labelmap-and-scalar-volume-not-the-same/4522)

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**Author:** [@mag](https://discourse.slicer.org/u/mag)\
**Replies:** 1\
**Last updated:** [October 25, 2018, 2:42am UTC](https://discourse.slicer.org/t/why-is-size-shape-of-numpy-array-from-labelmap-and-scalar-volume-not-the-same/4522 "2018-10-25T02:42:14Z")

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Hi, I want to export my volume and segmentation into numpy arrays so that I can use them for further analysis. I did as explained in this post and it seems to work but I don’t quite understand why the arrays I obtain do…

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## [I want to remove unnecessary artifacts of my 3D view of DICOM volume. I used segment editor but it does not work ( version 4.9)](https://discourse.slicer.org/t/i-want-to-remove-unnecessary-artifacts-of-my-3d-view-of-dicom-volume-i-used-segment-editor-but-it-does-not-work-version-4-9/4514)

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**Author:** [@M\_pavi](https://discourse.slicer.org/u/M_pavi)\
**Replies:** 0\
**Last updated:** [October 23, 2018, 9:31pm UTC](https://discourse.slicer.org/t/i-want-to-remove-unnecessary-artifacts-of-my-3d-view-of-dicom-volume-i-used-segment-editor-but-it-does-not-work-version-4-9/4514 "2018-10-23T21:31:18Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Using DICOM deformable registrations](https://discourse.slicer.org/t/using-dicom-deformable-registrations/4491)

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**Author:** [@stephan](https://discourse.slicer.org/u/stephan)\
**Replies:** 11\
**Last updated:** [October 24, 2018, 4:05pm UTC](https://discourse.slicer.org/t/using-dicom-deformable-registrations/4491 "2018-10-24T16:05:24Z")

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Slicer version: 4.10.0 SlicerRT: 0.18.0 Hi there, I wonder if there are known issues with loading deformable registration DICOM objects using SlicerRT. I have 2 CT volumes (“baseline” and “end”) which were registered…

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## [Moving slice intersection/crosshair over a fiducial point](https://discourse.slicer.org/t/moving-slice-intersection-crosshair-over-a-fiducial-point/4517)

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**Author:** [@mag](https://discourse.slicer.org/u/mag)\
**Replies:** 2\
**Last updated:** [October 24, 2018, 12:25pm UTC](https://discourse.slicer.org/t/moving-slice-intersection-crosshair-over-a-fiducial-point/4517 "2018-10-24T12:25:57Z")

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Hello, this is just a very minor issue but I am using Slicer a lot lately and it started bothering me a bit. When I display the slice intersection or the cross hair and use Shift-Key + mouse movements to scroll the sli…

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## [Preset for better visualization of bladder/prostate.](https://discourse.slicer.org/t/preset-for-better-visualization-of-bladder-prostate/4471)

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**Author:** [@AJR](https://discourse.slicer.org/u/AJR)\
**Replies:** 12\
**Last updated:** [October 23, 2018, 11:30pm UTC](https://discourse.slicer.org/t/preset-for-better-visualization-of-bladder-prostate/4471 "2018-10-23T23:30:05Z")

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As the title suggests, I am hoping to find a preset which will give me a better visualization of the bladder/prostate area. I’ve been searching all over and have so far been unsuccessful. 3d Slicer is a bit complex and…

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## [Mismatch of image and segmentation volume](https://discourse.slicer.org/t/mismatch-of-image-and-segmentation-volume/4493)

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**Author:** [@Gargi.Kothari](https://discourse.slicer.org/u/Gargi.Kothari)\
**Replies:** 6\
**Last updated:** [October 23, 2018, 9:46pm UTC](https://discourse.slicer.org/t/mismatch-of-image-and-segmentation-volume/4493 "2018-10-23T21:46:39Z")

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Operating system: Windows 7 Slicer version: 4.9.0 Expected behavior: Actual behavior: For some of the image datasets, the segmentation volume and CT sets are not registered correctly, but should have been on the origi…

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## [Grabbing the default segment editor widget](https://discourse.slicer.org/t/grabbing-the-default-segment-editor-widget/2375)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 3\
**Last updated:** [October 23, 2018, 9:25pm UTC](https://discourse.slicer.org/t/grabbing-the-default-segment-editor-widget/2375 "2018-10-23T21:25:29Z")

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Hi, Is there any way to access the active segment editor widget, for example to see the master volume / segmentation active currently? Thanks Usman.

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## [Documented threshold values for various body parts](https://discourse.slicer.org/t/documented-threshold-values-for-various-body-parts/4510)

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**Author:** [@EricWilson](https://discourse.slicer.org/u/EricWilson)\
**Replies:** 3\
**Last updated:** [October 23, 2018, 7:46pm UTC](https://discourse.slicer.org/t/documented-threshold-values-for-various-body-parts/4510 "2018-10-23T19:46:25Z")

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Hello, Is there some kind of documentation about exactly what threshold values to use on various body parts to get the best segments? if there is, how accurate is it, can it easily and cleanly separate things like skin…

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## [Are there any bone morphometry tools available for Slicer?](https://discourse.slicer.org/t/are-there-any-bone-morphometry-tools-available-for-slicer/4322)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 5\
**Last updated:** [October 23, 2018, 6:58pm UTC](https://discourse.slicer.org/t/are-there-any-bone-morphometry-tools-available-for-slicer/4322 "2018-10-23T18:58:32Z")

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For example, is this implemented or what would it take to make it available? Best

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## [VMTK extension for PCA](https://discourse.slicer.org/t/vmtk-extension-for-pca/4497)

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**Author:** [@14jwkn](https://discourse.slicer.org/u/14jwkn)\
**Replies:** 1\
**Last updated:** [October 23, 2018, 5:06pm UTC](https://discourse.slicer.org/t/vmtk-extension-for-pca/4497 "2018-10-23T17:06:13Z")

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Hello, I’m new to this and so far I’ve been using this tutorial (https://na-mic.org/w/images/a/aa/VMTK\_Slicer\_3.6.3\_Updated\_OCT\_2011.pdf). I’ve been trying to do a segmentation for the PCA on a t1 divided by t2 MRI scan.…

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## [Slicer Example Datasets](https://discourse.slicer.org/t/slicer-example-datasets/4501)

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**Author:** [@Matthew\_Hamilton](https://discourse.slicer.org/u/Matthew_Hamilton)\
**Replies:** 1\
**Last updated:** [October 23, 2018, 3:28pm UTC](https://discourse.slicer.org/t/slicer-example-datasets/4501 "2018-10-23T15:28:00Z")

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There is a Sample Data module included with Slicer. There is a notice that the “CTA Abdomen (Panoramix)” is only for research and teaching purposes and not for comercial purposes. Can anyone elaborate on the status of t…

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## [Import problem - MITK to Slicer](https://discourse.slicer.org/t/import-problem-mitk-to-slicer/4487)

<div class="topic-metadata">

**Author:** [@Maciej84](https://discourse.slicer.org/u/Maciej84)\
**Replies:** 2\
**Last updated:** [October 23, 2018, 11:04am UTC](https://discourse.slicer.org/t/import-problem-mitk-to-slicer/4487 "2018-10-23T11:04:33Z")

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Operating system: Win 10 Slicer version: 4.9.0 Expected behavior: Trying to import segmentations I made in MITK into slicer Actual behavior: Segmentations become ‘jaggedy’ - see screen grab below, particularly occipi…

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## [Crop volume to a single slice](https://discourse.slicer.org/t/crop-volume-to-a-single-slice/4483)

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**Author:** [@melsha3rawy](https://discourse.slicer.org/u/melsha3rawy)\
**Replies:** 3\
**Last updated:** [October 22, 2018, 10:53pm UTC](https://discourse.slicer.org/t/crop-volume-to-a-single-slice/4483 "2018-10-22T22:53:35Z")

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Operating system: win10 64bit Slicer version:4.10 Expected behavior: NA Actual behavior: can I crop one slice (dicom) to get a specific feature.

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