# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=352

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

**Page:** 353

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## [Scipy installation in slicer 4.10.1](https://discourse.slicer.org/t/scipy-installation-in-slicer-4-10-1/10369)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [February 20, 2020, 7:19pm UTC](https://discourse.slicer.org/t/scipy-installation-in-slicer-4-10-1/10369 "2020-02-20T19:19:31Z")

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Operating system: Linux Slicer version: 4.10.1 Hi 3D Slicer experts and all I want to install Scipy using pip.main(\[‘install’, ‘scipy’\]) , but I get an error, as shown in the following figure. Can you help me with thi…

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## [3D label map and the 3D view of segmentation mismatch](https://discourse.slicer.org/t/3d-label-map-and-the-3d-view-of-segmentation-mismatch/10356)

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**Author:** [@Mohammad\_Tanjib\_Rahm](https://discourse.slicer.org/u/Mohammad_Tanjib_Rahm)\
**Replies:** 5\
**Last updated:** [February 20, 2020, 4:27pm UTC](https://discourse.slicer.org/t/3d-label-map-and-the-3d-view-of-segmentation-mismatch/10356 "2020-02-20T16:27:25Z")

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Hi all, I am trying to do segmentation using MRI data. After completing the segmentation I saved it as a label map to view it as voxels instead of tetrahedral meshes. The problem is there are small holes at the bottom o…

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## [Siemens PET/CT files](https://discourse.slicer.org/t/siemens-pet-ct-files/2049)

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**Author:** [@Hamburgerfinger](https://discourse.slicer.org/u/Hamburgerfinger)\
**Replies:** 6\
**Last updated:** [February 20, 2020, 4:29am UTC](https://discourse.slicer.org/t/siemens-pet-ct-files/2049 "2020-02-20T04:29:05Z")

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Can Slicer directly load Siemens PET/CT images? (.img and .hdr files) I can get them into Slicer by exporting them from Siemens’ software in dicom format, but it would be much more convenient to import them into Slicer d…

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## [Surface Scan Registration](https://discourse.slicer.org/t/surface-scan-registration/10345)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 4\
**Last updated:** [February 20, 2020, 3:52am UTC](https://discourse.slicer.org/t/surface-scan-registration/10345 "2020-02-20T03:52:50Z")

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Dear all, This is again regarding surface scan registration issues with 3Shape Trios scans. The scan output is “stl” when we try to superimposes the scans again it is very very difficult with 3D Slicer. We used the Ge…

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## [Spanish Characters](https://discourse.slicer.org/t/spanish-characters/10333)

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**Author:** [@Pablo\_de\_Arriba](https://discourse.slicer.org/u/Pablo_de_Arriba)\
**Replies:** 3\
**Last updated:** [February 20, 2020, 3:45am UTC](https://discourse.slicer.org/t/spanish-characters/10333 "2020-02-20T03:45:41Z")

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In the beginning of the code write (in the first line): # -- coding: 850 -- Then, you can use the characters as follows (unicode): \\xe1 = á \\xe9 = é \\xed = í \\xf3 = ó \\xfa = ú \\xc1 = Á \\xc9 = É \\xcd = Í \\xd3 =…

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## [Centerline options and best way to measure arterial vessels?](https://discourse.slicer.org/t/centerline-options-and-best-way-to-measure-arterial-vessels/10234)

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**Author:** [@Romeo\_Guevara](https://discourse.slicer.org/u/Romeo_Guevara)\
**Replies:** 8\
**Last updated:** [February 19, 2020, 4:49pm UTC](https://discourse.slicer.org/t/centerline-options-and-best-way-to-measure-arterial-vessels/10234 "2020-02-19T16:49:31Z")

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Good evening, how can I make the axial cut, when shown in the “3D only” follow the center line I made? that in order to measure the diameter of the vessels as well as possible.

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## [Extensions build error (e.g. SlicerJupyter)](https://discourse.slicer.org/t/extensions-build-error-e-g-slicerjupyter/10346)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 3\
**Last updated:** [February 19, 2020, 1:14am UTC](https://discourse.slicer.org/t/extensions-build-error-e-g-slicerjupyter/10346 "2020-02-19T01:14:39Z")

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Hi, I wanted to update my Slicer Preview version. I need the SlicerJupyter extension, but I noticed that it has build errors for a couple of weeks now. I went back in the CDash calendar to a date when it was built, but …

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## [Class/syntax change for segmentation (slicer 4.10- 4.11)](https://discourse.slicer.org/t/class-syntax-change-for-segmentation-slicer-4-10-4-11/10238)

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**Author:** [@prorai](https://discourse.slicer.org/u/prorai)\
**Replies:** 16\
**Last updated:** [February 18, 2020, 3:21pm UTC](https://discourse.slicer.org/t/class-syntax-change-for-segmentation-slicer-4-10-4-11/10238 "2020-02-18T15:21:31Z")

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what are the changes in class and its parameters? ExportAllSegmentsToModelHierarchy() is now ExportAllSegmentsToModels() , i believe its right. But what is vtkIdType folderItemId ? what should i pass here?

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## [Cannot store MultiVolumeExplorer chart to .svg](https://discourse.slicer.org/t/cannot-store-multivolumeexplorer-chart-to-svg/10245)

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**Author:** [@nwschurink](https://discourse.slicer.org/u/nwschurink)\
**Replies:** 3\
**Last updated:** [February 18, 2020, 1:53pm UTC](https://discourse.slicer.org/t/cannot-store-multivolumeexplorer-chart-to-svg/10245 "2020-02-18T13:53:45Z")

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Operating system: Windows 7 Enterprise 64-bit (6.1, Build 7601) Slicer version: version 4.10.2 revision 28257 built 2019-05-22 Expected behavior: I am using the MultiVolumeExporer to extract a time intensity curve of …

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## [Create 1 model out of 3 volumes with different kernels](https://discourse.slicer.org/t/create-1-model-out-of-3-volumes-with-different-kernels/10332)

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**Author:** [@zeliair](https://discourse.slicer.org/u/zeliair)\
**Replies:** 1\
**Last updated:** [February 18, 2020, 1:26pm UTC](https://discourse.slicer.org/t/create-1-model-out-of-3-volumes-with-different-kernels/10332 "2020-02-18T13:26:46Z")

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Hey! I want to do threshold segmentation of the cranium. We found 2 different Kernels, one shows the teeth perfectly, the other one the cranial base. Now I want to merge the two Kernels into 1 model ! Is this possibl…

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## [Radiomics in dicom and nrrd](https://discourse.slicer.org/t/radiomics-in-dicom-and-nrrd/10265)

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**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 4\
**Last updated:** [February 18, 2020, 9:30am UTC](https://discourse.slicer.org/t/radiomics-in-dicom-and-nrrd/10265 "2020-02-18T09:30:55Z")

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Hi, I am doing a small radiomics study on clinical patients. The way I did it is imported dicom via “Load Data” in 3d Slicer and then saved the volume and segmentation as nrrd files. After that I did a batch processing.…

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## [How to define vessel centerline](https://discourse.slicer.org/t/how-to-define-vessel-centerline/9042)

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**Author:** [@Romeo\_Guevara](https://discourse.slicer.org/u/Romeo_Guevara)\
**Replies:** 2\
**Last updated:** [February 18, 2020, 9:05am UTC](https://discourse.slicer.org/t/how-to-define-vessel-centerline/9042 "2020-02-18T09:05:26Z")

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## [New module for measuring user statistics](https://discourse.slicer.org/t/new-module-for-measuring-user-statistics/9220)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 5\
**Last updated:** [February 18, 2020, 2:28am UTC](https://discourse.slicer.org/t/new-module-for-measuring-user-statistics/9220 "2020-02-18T02:28:48Z")

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In the latest 3D Slicer 4.11.0 releases, the SlicerSandbox extension now includes the “User Statistics” module for measuring how much time is spent using various tools in Slicer. This can be useful for getting quantitati…

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## [Saved pial surface model reloads as invalid](https://discourse.slicer.org/t/saved-pial-surface-model-reloads-as-invalid/10268)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 6\
**Last updated:** [February 17, 2020, 6:33pm UTC](https://discourse.slicer.org/t/saved-pial-surface-model-reloads-as-invalid/10268 "2020-02-17T18:33:00Z")

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Hello, I use FreeSurfer to generate cortical surface models from a brain MR volume (outside of Slicer). Slicer can load the resulting surface files (lh.pial and rh.pial) as models and they seem to function as normal mod…

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## [High definition segmentation](https://discourse.slicer.org/t/high-definition-segmentation/10310)

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**Author:** [@ThomPote](https://discourse.slicer.org/u/ThomPote)\
**Replies:** 1\
**Last updated:** [February 17, 2020, 2:26pm UTC](https://discourse.slicer.org/t/high-definition-segmentation/10310 "2020-02-17T14:26:52Z")

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Hi, In addition to this topic Segmentation High resolution, what are the different methods to increase definition in segmentation ? How can we increase resolution ? How can we remedy to pixelated image on external…

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## [Cannot segment the inferior part of the volume](https://discourse.slicer.org/t/cannot-segment-the-inferior-part-of-the-volume/10306)

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**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\
**Replies:** 3\
**Last updated:** [February 17, 2020, 1:35pm UTC](https://discourse.slicer.org/t/cannot-segment-the-inferior-part-of-the-volume/10306 "2020-02-17T13:35:55Z")

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Hi everyone, In Segment Editor module, the inferior part of the volume cannot be segmented no matter in Scissors or Threshold effect (attached figure). Version: 4.11.0 System: Mac Best wishes, Xie

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## [How to extract brain to STL when I have 3 different files with one HD resolution in one direction each?](https://discourse.slicer.org/t/how-to-extract-brain-to-stl-when-i-have-3-different-files-with-one-hd-resolution-in-one-direction-each/10294)

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**Author:** [@meee](https://discourse.slicer.org/u/meee)\
**Replies:** 1\
**Last updated:** [February 16, 2020, 6:16pm UTC](https://discourse.slicer.org/t/how-to-extract-brain-to-stl-when-i-have-3-different-files-with-one-hd-resolution-in-one-direction-each/10294 "2020-02-16T18:16:12Z")

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Hello, I am trying to do it for such a long time and find no answer anywhere. I have few files from my brain MRI and I am trying to extract it to STL file so I can 3D print it. I have been trying to do it with FreeSur…

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## [Error message Dcm2niixplugin](https://discourse.slicer.org/t/error-message-dcm2niixplugin/10290)

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**Author:** [@HariES](https://discourse.slicer.org/u/HariES)\
**Replies:** 1\
**Last updated:** [February 16, 2020, 1:35pm UTC](https://discourse.slicer.org/t/error-message-dcm2niixplugin/10290 "2020-02-16T13:35:58Z")

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I am getting following message while loading dicom. Can you tell me how to rectify Dcm2niixplugin

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## [Apply transformation](https://discourse.slicer.org/t/apply-transformation/10278)

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**Author:** [@Adam1122](https://discourse.slicer.org/u/Adam1122)\
**Replies:** 3\
**Last updated:** [February 16, 2020, 10:56am UTC](https://discourse.slicer.org/t/apply-transformation/10278 "2020-02-16T10:56:30Z")

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Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffus…

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## [Custom Size Segment](https://discourse.slicer.org/t/custom-size-segment/10269)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 1\
**Last updated:** [February 16, 2020, 4:58am UTC](https://discourse.slicer.org/t/custom-size-segment/10269 "2020-02-16T04:58:42Z")

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Can some one please help me with in creating a custom Box shape area of segmentation like the Sphere in the “Manipulating objects in the slice viewer” ? Or is there a way to define the ROI and then create a segme…

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## [How to save my work into dicom format](https://discourse.slicer.org/t/how-to-save-my-work-into-dicom-format/10182)

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**Author:** [@prencekhan](https://discourse.slicer.org/u/prencekhan)\
**Replies:** 10\
**Last updated:** [February 14, 2020, 4:09am UTC](https://discourse.slicer.org/t/how-to-save-my-work-into-dicom-format/10182 "2020-02-14T04:09:54Z")

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Hello! I would like to ask how do I save my work into DICOM format? I need to save it into DICOM format because I will be import it to the treatment planning computer. Thanks for your help

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## [Curved Planar Reformat module reslicing error](https://discourse.slicer.org/t/curved-planar-reformat-module-reslicing-error/10248)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 0\
**Last updated:** [February 13, 2020, 10:19pm UTC](https://discourse.slicer.org/t/curved-planar-reformat-module-reslicing-error/10248 "2020-02-13T22:19:02Z")

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Hello, I use SplineDrivenImageSlicer via the Curve Planar Reformat module of Slicer. However, I noticed that when I tried to reslice along a curve that the resliced images are not exactly centered on the supplied curve. …

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## [Reslice / Reorient Slice view](https://discourse.slicer.org/t/reslice-reorient-slice-view/10093)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 24\
**Last updated:** [February 13, 2020, 8:31pm UTC](https://discourse.slicer.org/t/reslice-reorient-slice-view/10093 "2020-02-13T20:31:04Z")

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I have some micro CT data of dental implants. However the implants are not vertical in slice view and we need to define a ROI of in the micro thread area only. I wanted to define the ROI as follows But since there…

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## [Tooth segmentation](https://discourse.slicer.org/t/tooth-segmentation/10175)

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**Author:** [@flaviu2](https://discourse.slicer.org/u/flaviu2)\
**Replies:** 5\
**Last updated:** [February 13, 2020, 6:17pm UTC](https://discourse.slicer.org/t/tooth-segmentation/10175 "2020-02-13T18:17:35Z")

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I am struggling to find a segmentation solution to isolate from an CBCT a tooth from a teeth. But I didn’t found any example of how to do this using SimpleITK/ITK. Can you point me a starting of how to achieve this task …

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## [How to get onClick a qt.QComboBox() in a table?](https://discourse.slicer.org/t/how-to-get-onclick-a-qt-qcombobox-in-a-table/10222)

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**Author:** [@john123](https://discourse.slicer.org/u/john123)\
**Replies:** 2\
**Last updated:** [February 13, 2020, 5:57pm UTC](https://discourse.slicer.org/t/how-to-get-onclick-a-qt-qcombobox-in-a-table/10222 "2020-02-13T17:57:05Z")

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I am using qt.QTableWidget() with 2 columns. The first column contains checkbox, while the second column is a qt.QComboBox(). I want to get the event when the user select the item in the qt.QComboBox(). How should I achi…

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## [What's the recommended workflow to convert DICOM files into slices?](https://discourse.slicer.org/t/whats-the-recommended-workflow-to-convert-dicom-files-into-slices/10241)

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**Author:** [@AmateurRadiologist](https://discourse.slicer.org/u/AmateurRadiologist)\
**Replies:** 3\
**Last updated:** [February 13, 2020, 3:26pm UTC](https://discourse.slicer.org/t/whats-the-recommended-workflow-to-convert-dicom-files-into-slices/10241 "2020-02-13T15:26:27Z")

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First the bragging I am the proud owner of a Faxitron MX-20 X-ray cabinet, equipped with a 20μm spot size micro-focus tube, with a fixed beam current at 300μA, a voltage anywhere between 10 and 35kV and an exposure time…

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## [Listing of known working GPU card and associated datasets](https://discourse.slicer.org/t/listing-of-known-working-gpu-card-and-associated-datasets/8009)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 8\
**Last updated:** [February 13, 2020, 2:13pm UTC](https://discourse.slicer.org/t/listing-of-known-working-gpu-card-and-associated-datasets/8009 "2020-02-13T14:13:15Z")

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To help Slicer users understand which graphics card works best for which tasks, I would appreciate if you could comment below with details like: Slicer version GPU card description (name, memory, …) Operating System, C…

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## [Python : how to centre volume on load?](https://discourse.slicer.org/t/python-how-to-centre-volume-on-load/10220)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 5\
**Last updated:** [February 13, 2020, 1:42pm UTC](https://discourse.slicer.org/t/python-how-to-centre-volume-on-load/10220 "2020-02-13T13:42:48Z")

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Previously, using the ‘Add data’ menu, we would check the ‘Centre’ widget so that the loaded volume (DICOM series) was centered. The ‘Add data’ menu is no longer maintained for this use, and I’m using the DICOM module in…

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## [Validation papers for SlicerRT?](https://discourse.slicer.org/t/validation-papers-for-slicerrt/10224)

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**Author:** [@stephan](https://discourse.slicer.org/u/stephan)\
**Replies:** 1\
**Last updated:** [February 13, 2020, 9:12am UTC](https://discourse.slicer.org/t/validation-papers-for-slicerrt/10224 "2020-02-13T09:12:35Z")

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Hi @cpinter and @lassoan, I am writing a manuscript where the methods are heavily based on SlicerRT. I am citing your 2012 Medical Physics paper, for sure. But I was wondering if any other papers have come out in the …

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## [NRRD scale factor](https://discourse.slicer.org/t/nrrd-scale-factor/10232)

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**Author:** [@Hamburgerfinger](https://discourse.slicer.org/u/Hamburgerfinger)\
**Replies:** 3\
**Last updated:** [February 13, 2020, 6:31am UTC](https://discourse.slicer.org/t/nrrd-scale-factor/10232 "2020-02-13T06:31:29Z")

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I’ve used RawImageGuess module to guess the format of some images and I’d like to use the ‘Generate nrrd header’ function to create a header template and convert them all to \*.nrrd with a script. How can I include a sca…

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