# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=382

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

**Page:** 383

---

## [Convert Matlab coordinates to Slicer](https://discourse.slicer.org/t/convert-matlab-coordinates-to-slicer/7163)

<div class="topic-metadata">

**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 7\
**Last updated:** [June 18, 2019, 7:24pm UTC](https://discourse.slicer.org/t/convert-matlab-coordinates-to-slicer/7163 "2019-06-18T19:24:00Z")

</div>

Hello, I would like to convert Matlab coordinates to Slicer. I load Dicom images to Matlab and I get some coordinates. Then, I try to load them on Slicer, but both are in a completely different position. Could you pl…

---

## [How to read the value of certain attribute (tag) in DICOM Metadata" from "Python Interactor"](https://discourse.slicer.org/t/how-to-read-the-value-of-certain-attribute-tag-in-dicom-metadata-from-python-interactor/7184)

<div class="topic-metadata">

**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 5\
**Last updated:** [June 18, 2019, 3:59pm UTC](https://discourse.slicer.org/t/how-to-read-the-value-of-certain-attribute-tag-in-dicom-metadata-from-python-interactor/7184 "2019-06-18T15:59:36Z")

</div>

Hi Dears 3DSlicer developers After loading dicom files using DICOM module, how can I access the value of certain attribute (tag) in “DICOM Metadata” from Python Interactor? For example, I want to access the value of Is…

---

## [Visualization of MRI’s of the lumbar and sacral vertebra](https://discourse.slicer.org/t/visualization-of-mri-s-of-the-lumbar-and-sacral-vertebra/7212)

<div class="topic-metadata">

**Author:** [@ProblemsStanding](https://discourse.slicer.org/u/ProblemsStanding)\
**Replies:** 1\
**Last updated:** [June 18, 2019, 3:40pm UTC](https://discourse.slicer.org/t/visualization-of-mri-s-of-the-lumbar-and-sacral-vertebra/7212 "2019-06-18T15:40:58Z")

</div>

Operating system: windos 10 and a brain not made for this. Slicer version: 4.10.2 Expected behavior: I want to make a 3D visualization from MRI’s of the lumbar and sacral vertebra with nerves, vessels, muscles levator …

---

## [Loading CT Perfusion images](https://discourse.slicer.org/t/loading-ct-perfusion-images/7220)

<div class="topic-metadata">

**Author:** [@Sibi\_Thirunavukarasu](https://discourse.slicer.org/u/Sibi_Thirunavukarasu)\
**Replies:** 0\
**Last updated:** [June 18, 2019, 3:05pm UTC](https://discourse.slicer.org/t/loading-ct-perfusion-images/7220 "2019-06-18T15:05:15Z")

</div>

Hi, I am unable to load CT perfusion images in the slicer. Should i use a specific module to open it? I should also coregister CT perfusion images to the MRI DWI. How do I do that? Thanks in advance

---

## [Extracting Data from VMTK Centerline](https://discourse.slicer.org/t/extracting-data-from-vmtk-centerline/7205)

<div class="topic-metadata">

**Author:** [@joshWilliams](https://discourse.slicer.org/u/joshWilliams)\
**Replies:** 3\
**Last updated:** [June 18, 2019, 2:39pm UTC](https://discourse.slicer.org/t/extracting-data-from-vmtk-centerline/7205 "2019-06-18T14:39:38Z")

</div>

Hi, I am using VMTK’s centreline computation tool to extract a skeleton of a respiratory system (from a stl file, converted to binary label map). I have previewed the skeleton and pressed start to begin extracting data …

---

## [What is different HU and voxel value](https://discourse.slicer.org/t/what-is-different-hu-and-voxel-value/7213)

<div class="topic-metadata">

**Author:** [@kscript](https://discourse.slicer.org/u/kscript)\
**Replies:** 1\
**Last updated:** [June 18, 2019, 3:17am UTC](https://discourse.slicer.org/t/what-is-different-hu-and-voxel-value/7213 "2019-06-18T03:17:55Z")

</div>

HI. 1. I open dicom file’s header using 3D Slicer. i can get LargestImagePixelValue and smallestImagePixelValue. 2. And I check Volumes’ Histogram using 3D Slicer. and I check HU(HounsField Unit) Range. but Two re…

---

## [Interpreting segmentation nrrd files](https://discourse.slicer.org/t/interpreting-segmentation-nrrd-files/1641)

<div class="topic-metadata">

**Author:** [@dcantor](https://discourse.slicer.org/u/dcantor)\
**Replies:** 10\
**Last updated:** [June 17, 2019, 5:57pm UTC](https://discourse.slicer.org/t/interpreting-segmentation-nrrd-files/1641 "2019-06-17T17:57:31Z")

</div>

Hello, I am segmenting prostates with Slicer and now I want to post-process my segmentations. So I read the nrrd segmentation files with my python code. I have a case where I have one file with one segmentation and two …

---

## [Change data-transform hierarchy nodes](https://discourse.slicer.org/t/change-data-transform-hierarchy-nodes/7187)

<div class="topic-metadata">

**Author:** [@zapaishchykova](https://discourse.slicer.org/u/zapaishchykova)\
**Replies:** 2\
**Last updated:** [June 17, 2019, 2:15pm UTC](https://discourse.slicer.org/t/change-data-transform-hierarchy-nodes/7187 "2019-06-17T14:15:39Z")

</div>

Hi there! I’m trying to find how can I with python change transform hierarchy of the scene, and all I was able to find is only how to change subject hierarchy: sceneItemID = shn.GetSceneItemID() shn = slicer.vtkMRMLSu…

---

## [Problem with VMTK for vessel segmentation](https://discourse.slicer.org/t/problem-with-vmtk-for-vessel-segmentation/7195)

<div class="topic-metadata">

**Author:** [@dongchenyang](https://discourse.slicer.org/u/dongchenyang)\
**Replies:** 1\
**Last updated:** [June 17, 2019, 5:33am UTC](https://discourse.slicer.org/t/problem-with-vmtk-for-vessel-segmentation/7195 "2019-06-17T05:33:03Z")

</div>

Hi, I am new to VMTK and I tried to follow the tutorial on https://na-mic.org/w/images/archive/4/40/20100107165806!TutorialVMTKCoronariesCenterlinesMRI\_Winter2010AHM.pdf, but the version they were using was too old and I…

---

## [Slicer can be installed without administrator privileges on Windows](https://discourse.slicer.org/t/slicer-can-be-installed-without-administrator-privileges-on-windows/7137)

<div class="topic-metadata">

**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 1\
**Last updated:** [June 17, 2019, 1:40am UTC](https://discourse.slicer.org/t/slicer-can-be-installed-without-administrator-privileges-on-windows/7137 "2019-06-17T01:40:40Z")

</div>

Starting from tomorrow, Slicer-4.11.x versions will not require administrator privileges for installation on Windows. The change was motivated by requests to make it easier to install Slicer in locked-down environments,…

---

## [Problem to build Slicer?!](https://discourse.slicer.org/t/problem-to-build-slicer/7177)

<div class="topic-metadata">

**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 3\
**Last updated:** [June 16, 2019, 7:49pm UTC](https://discourse.slicer.org/t/problem-to-build-slicer/7177 "2019-06-16T19:49:27Z")

</div>

Hi Dears 3DSlicer developers I want to build Slicer as mentioned in the site of https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build\_Instructions. I do the following steps: (base) \[sn@localhost ~\]$ uname…

---

## [Volume rendering](https://discourse.slicer.org/t/volume-rendering/7156)

<div class="topic-metadata">

**Author:** [@Manoj\_Bagare](https://discourse.slicer.org/u/Manoj_Bagare)\
**Replies:** 2\
**Last updated:** [June 13, 2019, 11:43am UTC](https://discourse.slicer.org/t/volume-rendering/7156 "2019-06-13T11:43:09Z")

</div>

Operating system:windows 10 Slicer version:4.11.0 Expected behavior: during volume rendering it should show the 3D model Actual behavior: when i click eye icon for volume rendering, the software close off itself durin…

---

## [Limited Fast marching range](https://discourse.slicer.org/t/limited-fast-marching-range/7176)

<div class="topic-metadata">

**Author:** [@Amine](https://discourse.slicer.org/u/Amine)\
**Replies:** 2\
**Last updated:** [June 16, 2019, 12:36am UTC](https://discourse.slicer.org/t/limited-fast-marching-range/7176 "2019-06-16T00:36:03Z")

</div>

Windows 10 Tried on Slicer 4.10.1 and 4.11 For this particular volume Fastmarching gets limited by an upper and lower limit ( i run it at a high “max volume” to better show its limits). Already tried: -Make sure the …

---

## [Infarct Segmentation combining b1000 and ADC](https://discourse.slicer.org/t/infarct-segmentation-combining-b1000-and-adc/7181)

<div class="topic-metadata">

**Author:** [@Sibi\_Thirunavukarasu](https://discourse.slicer.org/u/Sibi_Thirunavukarasu)\
**Replies:** 1\
**Last updated:** [June 15, 2019, 6:08pm UTC](https://discourse.slicer.org/t/infarct-segmentation-combining-b1000-and-adc/7181 "2019-06-15T18:08:31Z")

</div>

Hi, I would like to know if I can combine two mri sequences for segmentation process. Currently I am using one sequence for this purpose.

---

## [How to get SlicerRT runing on my Developer Installation?](https://discourse.slicer.org/t/how-to-get-slicerrt-runing-on-my-developer-installation/5440)

<div class="topic-metadata">

**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 8\
**Last updated:** [June 15, 2019, 2:06am UTC](https://discourse.slicer.org/t/how-to-get-slicerrt-runing-on-my-developer-installation/5440 "2019-06-15T02:06:52Z")

</div>

Operating system: Linux Slicer version: Slicer 4.9 Hi Everyone, I’d like to know how to install SlicerRT from source (GitHub) into my home Developer Installation. Thank you all!

---

## [Why is the number of voxels different from the number of matrices?](https://discourse.slicer.org/t/why-is-the-number-of-voxels-different-from-the-number-of-matrices/7134)

<div class="topic-metadata">

**Author:** [@kscript](https://discourse.slicer.org/u/kscript)\
**Replies:** 6\
**Last updated:** [June 14, 2019, 5:32am UTC](https://discourse.slicer.org/t/why-is-the-number-of-voxels-different-from-the-number-of-matrices/7134 "2019-06-14T05:32:29Z")

</div>

Hello everybody I am working on making the volume data of the segmentation nrrd extension an Array List. I have solved the method of creating an Array, but there is one question. The size of the image I use is 501x501…

---

## [virtualGL issue with nightly](https://discourse.slicer.org/t/virtualgl-issue-with-nightly/5050)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [June 13, 2019, 10:47pm UTC](https://discourse.slicer.org/t/virtualgl-issue-with-nightly/5050 "2019-06-13T22:47:49Z")

</div>

We have been using vgl to run Slicer remotely with HW acceleration on a Linux server quite a while now. I just installed one of the nightly from 12/06 and I am getting a blank Slicer window with these errors \[maga@maga…

---

## [Changing the header of images](https://discourse.slicer.org/t/changing-the-header-of-images/7152)

<div class="topic-metadata">

**Author:** [@pouyahoseini](https://discourse.slicer.org/u/pouyahoseini)\
**Replies:** 1\
**Last updated:** [June 13, 2019, 4:16pm UTC](https://discourse.slicer.org/t/changing-the-header-of-images/7152 "2019-06-13T16:16:20Z")

</div>

Operating system: windows 10 Slicer version:4.10.2 HI 3dslicer experts. I have two images , T1 and DWI , that have different isocenter.i want to changing DWI image’s Header to same of T1 image header.can you help me a…

---

## [Windows nightly extensions are late today](https://discourse.slicer.org/t/windows-nightly-extensions-are-late-today/7161)

<div class="topic-metadata">

**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [June 13, 2019, 3:28pm UTC](https://discourse.slicer.org/t/windows-nightly-extensions-are-late-today/7161 "2019-06-13T15:28:16Z")

</div>

Hi all: Due to some issues on the windows factory, we have had to re-trigger the nightly extension builds. So extensions will be coming online over the next hours. The windows nightly installer is available now, at do…

---

## [NAC Brain Atlas 2015 from Data Store is giving scene hierarchy errors after loading](https://discourse.slicer.org/t/nac-brain-atlas-2015-from-data-store-is-giving-scene-hierarchy-errors-after-loading/7160)

<div class="topic-metadata">

**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 1\
**Last updated:** [June 13, 2019, 3:16pm UTC](https://discourse.slicer.org/t/nac-brain-atlas-2015-from-data-store-is-giving-scene-hierarchy-errors-after-loading/7160 "2019-06-13T15:16:59Z")

</div>

Hello, the NAC Brain Atlas 2015 from the Data Store loads without errors, but after trying to load one of the saved scene views from that mrb, Slicer 4.10.1 reports the following errors and the Subject Hierarchy in the D…

---

## [How to quantitatively compare SPM fMRI data and BIP maps](https://discourse.slicer.org/t/how-to-quantitatively-compare-spm-fmri-data-and-bip-maps/7140)

<div class="topic-metadata">

**Author:** [@carba86](https://discourse.slicer.org/u/carba86)\
**Replies:** 3\
**Last updated:** [June 13, 2019, 2:35pm UTC](https://discourse.slicer.org/t/how-to-quantitatively-compare-spm-fmri-data-and-bip-maps/7140 "2019-06-13T14:35:24Z")

</div>

I am currently working with fMRI, trying to compare performance between SPM and the software provided by GE, BrainWave PA. Besides comparing the two sets of post-processed images with two senior radiologists, I would lik…

---

## [Load LabelMap volume](https://discourse.slicer.org/t/load-labelmap-volume/7155)

<div class="topic-metadata">

**Author:** [@thu.nguyen](https://discourse.slicer.org/u/thu.nguyen)\
**Replies:** 2\
**Last updated:** [June 13, 2019, 11:52am UTC](https://discourse.slicer.org/t/load-labelmap-volume/7155 "2019-06-13T11:52:19Z")

</div>

Operating system: Mac Os 10.11.6 Slicer version: 4.8.1, 4.10.0, 4.10.2 Expected behavior: Load a Nifti file (unsigned char) as LabelMap volume Actual behavior: 3DSlicer does nothing, even when the LabelMap option is n…

---

## [Segmenting fractured bone fragments](https://discourse.slicer.org/t/segmenting-fractured-bone-fragments/3575)

<div class="topic-metadata">

**Author:** [@Shamay\_Agaron](https://discourse.slicer.org/u/Shamay_Agaron)\
**Replies:** 5\
**Last updated:** [June 12, 2019, 3:05pm UTC](https://discourse.slicer.org/t/segmenting-fractured-bone-fragments/3575 "2019-06-12T15:05:08Z")

</div>

I was wondering if anyone can recommend a semi-automatic way to separate different fractured bone fragments. I’ve been trying to use the various functions available in Segment Editor and it’s extension, but the main i…

---

## [Import of ITK transform file failed](https://discourse.slicer.org/t/import-of-itk-transform-file-failed/7126)

<div class="topic-metadata">

**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 5\
**Last updated:** [June 12, 2019, 2:30pm UTC](https://discourse.slicer.org/t/import-of-itk-transform-file-failed/7126 "2019-06-12T14:30:16Z")

</div>

Hi, I am trying to import an affine transform that was computed with ANTs. I cannot attach the transform file, but it is a simple textfile with a .txt file ending. You can reproduce the error by copy&pasting the content…

---

## [Reload button loads dependent modules](https://discourse.slicer.org/t/reload-button-loads-dependent-modules/7135)

<div class="topic-metadata">

**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 1\
**Last updated:** [June 12, 2019, 1:56pm UTC](https://discourse.slicer.org/t/reload-button-loads-dependent-modules/7135 "2019-06-12T13:56:57Z")

</div>

It would be nice to have the feature in the title. My workaround is to modify the file bin/python/slicer/ScriptedLoadableModule.py and add these lines in onReload(self) function myM…

---

## [Canon aplio 500 and vicon bonita system (nexus)](https://discourse.slicer.org/t/canon-aplio-500-and-vicon-bonita-system-nexus/7136)

<div class="topic-metadata">

**Author:** [@Ylim](https://discourse.slicer.org/u/Ylim)\
**Replies:** 0\
**Last updated:** [June 12, 2019, 1:49pm UTC](https://discourse.slicer.org/t/canon-aplio-500-and-vicon-bonita-system-nexus/7136 "2019-06-12T13:49:37Z")

</div>

I have an ultrasound aplio 500 and a vicon bonita here and would like to use slicer to reconstruct ultrasound data in 3d either in real time or post processing. I do not have tracker license. Any advice.

---

## [Importing segmentation into 3d slicer](https://discourse.slicer.org/t/importing-segmentation-into-3d-slicer/7080)

<div class="topic-metadata">

**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 10\
**Last updated:** [June 12, 2019, 7:33am UTC](https://discourse.slicer.org/t/importing-segmentation-into-3d-slicer/7080 "2019-06-12T07:33:54Z")

</div>

Hi, I am Tenzin. I would like to ask about a problem I am having. I did some segmentation on ITK snap and exported into nrrd format file. when I imported that into 3d slicer against a same volume, the segmentation is i…

---

## [How to import the nifti file of HCP842 Tractography Atlas to 3DSlicer as label maps?](https://discourse.slicer.org/t/how-to-import-the-nifti-file-of-hcp842-tractography-atlas-to-3dslicer-as-label-maps/7102)

<div class="topic-metadata">

**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 2\
**Last updated:** [June 11, 2019, 8:48pm UTC](https://discourse.slicer.org/t/how-to-import-the-nifti-file-of-hcp842-tractography-atlas-to-3dslicer-as-label-maps/7102 "2019-06-11T20:48:00Z")

</div>

Dears 3DSlicer developers: How can I use HCP842 Tractography Atlas to extract “fiber bundles” in DWI images. I want to use 80 regions segmented in this atlas as “Label Maps” in UKF Tractography. I must mentioned that …

---

## [Can't display two different segmentations in two slice views](https://discourse.slicer.org/t/cant-display-two-different-segmentations-in-two-slice-views/7119)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [June 11, 2019, 2:44pm UTC](https://discourse.slicer.org/t/cant-display-two-different-segmentations-in-two-slice-views/7119 "2019-06-11T14:44:35Z")

</div>

I have two volumes (volume1, volume2) and their respective segmentations (segmentation\_1, segmentation\_2). I couldn’t figure out how to have red slice view display the volume\_1 and segmentation\_1, while yellow slice vie…

---

## [Segmentation and nii file](https://discourse.slicer.org/t/segmentation-and-nii-file/7118)

<div class="topic-metadata">

**Author:** [@marline19](https://discourse.slicer.org/u/marline19)\
**Replies:** 1\
**Last updated:** [June 11, 2019, 1:57pm UTC](https://discourse.slicer.org/t/segmentation-and-nii-file/7118 "2019-06-11T13:57:52Z")

</div>

Hello everyone. May I made segmentation from nordicICE programm and than load it to 3D slicer? How can i load nii file to 3 Dslicer?

[Previous page](https://discourse.slicer.org/c/support/11.md?page=381)

[Next page](https://discourse.slicer.org/c/support/11.md?page=383)