# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=424

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

**Page:** 425

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## [Markups placement not displaying in a scene without any data](https://discourse.slicer.org/t/markups-placement-not-displaying-in-a-scene-without-any-data/2796)

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**Author:** [@roozbehshams](https://discourse.slicer.org/u/roozbehshams)\
**Replies:** 1\
**Last updated:** [May 14, 2018, 3:14am UTC](https://discourse.slicer.org/t/markups-placement-not-displaying-in-a-scene-without-any-data/2796 "2018-05-14T03:14:25Z")

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I’ve realized when trying to add markups fiducials in persistent mode, the display is not updated properly. This happens only when there is no data in the scene. When adding fiducials, they won’t show up unless: A fid…

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## [Start programming in Slicer: Transforms module, Elastix](https://discourse.slicer.org/t/start-programming-in-slicer-transforms-module-elastix/2499)

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**Author:** [@hadasara](https://discourse.slicer.org/u/hadasara)\
**Replies:** 16\
**Last updated:** [May 14, 2018, 2:57am UTC](https://discourse.slicer.org/t/start-programming-in-slicer-transforms-module-elastix/2499 "2018-05-14T02:57:26Z")

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Hi, I’m new in slicer so I have beginners questions: I’d like to use slicer modules through python programming, which I see in many places that is possible, just not sure how to get started. I don’t want to work through…

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## [Volume calculation of Models](https://discourse.slicer.org/t/volume-calculation-of-models/1482)

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**Author:** [@Remco](https://discourse.slicer.org/u/Remco)\
**Replies:** 6\
**Last updated:** [May 11, 2018, 6:30am UTC](https://discourse.slicer.org/t/volume-calculation-of-models/1482 "2018-05-11T06:30:47Z")

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Operating system: Win7 Slicer version: 4.9.0-2017-11-16 I have loaded a uMRI dataset and created some surface meshes using the segment editor. I would like to interrogate the volume of the surface meshes using the Mode…

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## [Slicer 4.8.1 crashes upon loading a volume](https://discourse.slicer.org/t/slicer-4-8-1-crashes-upon-loading-a-volume/2789)

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**Author:** [@zjx1805](https://discourse.slicer.org/u/zjx1805)\
**Replies:** 7\
**Last updated:** [May 10, 2018, 2:43pm UTC](https://discourse.slicer.org/t/slicer-4-8-1-crashes-upon-loading-a-volume/2789 "2018-05-10T14:43:02Z")

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I am having trouble loading a volume into slicer 4.8.1 on my desktop. Adding the volume through ‘Data’ module is fine and the slice views also show up correctly. However, the slicer will crash most of the time after I cl…

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## [Compiling slicer](https://discourse.slicer.org/t/compiling-slicer/2794)

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**Author:** [@vegoria](https://discourse.slicer.org/u/vegoria)\
**Replies:** 1\
**Last updated:** [May 10, 2018, 1:45pm UTC](https://discourse.slicer.org/t/compiling-slicer/2794 "2018-05-10T13:45:26Z")

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Hi. I’m trying to compile slicer (using linux mint). And keep getting error: CMakeFiles/N4ITKBiasFieldCorrectionLib.dir/N4ITKBiasFieldCorrection.cxx.o: In function ModuleEntryPoint': N4ITKBiasFieldCorrection.cxx:(.text…

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## [How to move the fiducials again?](https://discourse.slicer.org/t/how-to-move-the-fiducials-again/2770)

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**Author:** [@esurechao](https://discourse.slicer.org/u/esurechao)\
**Replies:** 5\
**Last updated:** [May 8, 2018, 2:19pm UTC](https://discourse.slicer.org/t/how-to-move-the-fiducials-again/2770 "2018-05-08T14:19:19Z")

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Operating system: windows 10 Slicer version: 4.6.2 I am trying to obtain the 3D coordinates of the organ landmarks. These are my steps: Load CT DICOM files Use segment editor module to visualize the structure in th…

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## [issues viewing DICOM files after import](https://discourse.slicer.org/t/issues-viewing-dicom-files-after-import/2768)

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**Author:** [@goetzf](https://discourse.slicer.org/u/goetzf)\
**Replies:** 4\
**Last updated:** [May 7, 2018, 8:36pm UTC](https://discourse.slicer.org/t/issues-viewing-dicom-files-after-import/2768 "2018-05-07T20:36:07Z")

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I have been following tutorials on how to load DICOM data and I can’t figure out why my data look weird. The scans were done with a GE vtome (not sure of all the specifics) and a nano-scale tube. The .dcm files were outp…

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## [How does Slicer finds the optimal viewing window (min/max values) when importing nifti file?](https://discourse.slicer.org/t/how-does-slicer-finds-the-optimal-viewing-window-min-max-values-when-importing-nifti-file/2763)

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**Author:** [@NaglisR](https://discourse.slicer.org/u/NaglisR)\
**Replies:** 1\
**Last updated:** [May 6, 2018, 3:45pm UTC](https://discourse.slicer.org/t/how-does-slicer-finds-the-optimal-viewing-window-min-max-values-when-importing-nifti-file/2763 "2018-05-06T15:45:39Z")

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Hi, I want to find out how does Slicer determines the optimal viewing window (min/max values) when importing nifti file. I know that when importing dicoms the windowing info is in the metadata, however as far as I know …

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## [How to analysis fmri data?](https://discourse.slicer.org/t/how-to-analysis-fmri-data/1553)

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**Author:** [@Jin](https://discourse.slicer.org/u/Jin)\
**Replies:** 6\
**Last updated:** [May 6, 2018, 1:42pm UTC](https://discourse.slicer.org/t/how-to-analysis-fmri-data/1553 "2018-05-06T13:42:28Z")

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Operating system:windows 10 enterprise Slicer version:4.8 Expected behavior: analaysis fMRI datas Actual behavior: I got the fMRI datas from the GE 3.0T MR, I want to analysis the datas. But I dont kown how to do, an…

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## [Slicer nightly version does not launch on windows](https://discourse.slicer.org/t/slicer-nightly-version-does-not-launch-on-windows/2758)

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**Author:** [@zjx1805](https://discourse.slicer.org/u/zjx1805)\
**Replies:** 6\
**Last updated:** [May 4, 2018, 4:18pm UTC](https://discourse.slicer.org/t/slicer-nightly-version-does-not-launch-on-windows/2758 "2018-05-04T16:18:14Z")

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I installed the latest nightly build (v4.9.0, built on 05/02) on my desktop and when I opened it, it disappeared after just showing a loading screen. I tried a dozen of times, and only for one time it launched, but the i…

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## [How to open Analyze format files in Slicer](https://discourse.slicer.org/t/how-to-open-analyze-format-files-in-slicer/2752)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 3\
**Last updated:** [May 4, 2018, 8:48am UTC](https://discourse.slicer.org/t/how-to-open-analyze-format-files-in-slicer/2752 "2018-05-04T08:48:41Z")

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Hi, I have a series of files saved as separate .img and .hdr files (analyze). When i load them using add data dialog, i get an error: ‘Could not read scalar volme using DCMTK / GDCM appraoch Error is fileformat’ Any t…

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## [Export CT-AAA2 from 3d Slicer](https://discourse.slicer.org/t/export-ct-aaa2-from-3d-slicer/2757)

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**Author:** [@ghoulfool](https://discourse.slicer.org/u/ghoulfool)\
**Replies:** 2\
**Last updated:** [May 4, 2018, 1:33am UTC](https://discourse.slicer.org/t/export-ct-aaa2-from-3d-slicer/2757 "2018-05-04T01:33:06Z")

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Operating system: Win 7 Slicer version:4.8.1 Expected behavior: Export an OBJ (as seen on screen) Actual behavior:No option to export (or in one case a 0 byes .OBJ) Hi, first time caller and I’m having problems expor…

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## [Volume rendering - crop not working in latest nightlies when loading older file](https://discourse.slicer.org/t/volume-rendering-crop-not-working-in-latest-nightlies-when-loading-older-file/2749)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 11\
**Last updated:** [May 3, 2018, 7:34pm UTC](https://discourse.slicer.org/t/volume-rendering-crop-not-working-in-latest-nightlies-when-loading-older-file/2749 "2018-05-03T19:34:50Z")

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This is on MacOS 10.12.6, MacBook Pro 15 retina (mid 2015), Radeon R9 M370X graphics. I have a project (MRML, NRRD, segmentation, etc) that I’ve been working with in the April 15 nightly build. I’ve set up volume render…

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## [Error when using filters](https://discourse.slicer.org/t/error-when-using-filters/2732)

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**Author:** [@FungalSlicer](https://discourse.slicer.org/u/FungalSlicer)\
**Replies:** 3\
**Last updated:** [May 3, 2018, 11:45am UTC](https://discourse.slicer.org/t/error-when-using-filters/2732 "2018-05-03T11:45:39Z")

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Hey guys, maybe someone has an idea about this sort or error, which I get when using some basic image filters: Median Image Filter standard error: Median Image Filter standard error: C:/Program Files/Slicer3D/Slicer …

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## [Ac-pc based registration](https://discourse.slicer.org/t/ac-pc-based-registration/2733)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 5\
**Last updated:** [May 3, 2018, 10:18am UTC](https://discourse.slicer.org/t/ac-pc-based-registration/2733 "2018-05-03T10:18:26Z")

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Hello 3d Slicer forum, I’d like to register two different images based on aligning the ac-pc lines. What is the best way to do this? Usually, I would do a nonlinear normalization of the moving image (atlas) to the fix…

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## [Is there any method to convert volume to DiffusionTensorvolume?](https://discourse.slicer.org/t/is-there-any-method-to-convert-volume-to-diffusiontensorvolume/2553)

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**Author:** [@ElonKou](https://discourse.slicer.org/u/ElonKou)\
**Replies:** 12\
**Last updated:** [May 3, 2018, 3:39am UTC](https://discourse.slicer.org/t/is-there-any-method-to-convert-volume-to-diffusiontensorvolume/2553 "2018-05-03T03:39:56Z")

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I am using dti to reconstruct Neurological plexus. and I load the data from dicom, the type of “node” is volume ,it 's not what I need(DiffusionTensorVolume). how could I convert this type ? The dti folder was load…

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## [Problems with Tractography to mask image ](https://discourse.slicer.org/t/problems-with-tractography-to-mask-image/2663)

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**Author:** [@punadkat](https://discourse.slicer.org/u/punadkat)\
**Replies:** 4\
**Last updated:** [May 2, 2018, 10:43pm UTC](https://discourse.slicer.org/t/problems-with-tractography-to-mask-image/2663 "2018-05-02T22:43:13Z")

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Hello, I am trying to convert fiber bundles to label maps. However, when I use the ‘Tractography to mask image’ module, my slicer app crashes. I have tried this on multiple slicer versions with no luck (4.8.1, nightly b…

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## [Segment Editor and rotate/tumble/orbit function in 3D view](https://discourse.slicer.org/t/segment-editor-and-rotate-tumble-orbit-function-in-3d-view/2726)

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**Author:** [@nslizer](https://discourse.slicer.org/u/nslizer)\
**Replies:** 14\
**Last updated:** [May 2, 2018, 10:20pm UTC](https://discourse.slicer.org/t/segment-editor-and-rotate-tumble-orbit-function-in-3d-view/2726 "2018-05-02T22:20:54Z")

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I’ve just returned to using Slicer for 3D modelling. The new segment concept and its editor are amazing! But how to rotate/tumble/orbit the 3D view in editing mode? The left-button is taken over by the paint function. I…

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## [Unable to load dicom into slicer](https://discourse.slicer.org/t/unable-to-load-dicom-into-slicer/2671)

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**Author:** [@b\_s\_umesh\_sherkhane](https://discourse.slicer.org/u/b_s_umesh_sherkhane)\
**Replies:** 2\
**Last updated:** [May 2, 2018, 10:31am UTC](https://discourse.slicer.org/t/unable-to-load-dicom-into-slicer/2671 "2018-05-02T10:31:54Z")

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Operating system: win7 Slicer version:4.8 Expected behavior: Actual behavior: “” Slicer has caught an internal error. You may be able to continue from this point, but results are undefined. Suggested action is to …

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## [Liver vasculature segmentation](https://discourse.slicer.org/t/liver-vasculature-segmentation/2688)

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**Author:** [@Serg](https://discourse.slicer.org/u/Serg)\
**Replies:** 1\
**Last updated:** [May 1, 2018, 11:39pm UTC](https://discourse.slicer.org/t/liver-vasculature-segmentation/2688 "2018-05-01T23:39:20Z")

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Hello, 3D Slicer team! We want to use 3D Slicer in a project where it is necessary to make a reconstruction of liver, tumor, and arteries similar to your recent manuscript (Utility of 3D Reconstruction of 2D Liver Compu…

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## [Use existing slicer modules with python and cli](https://discourse.slicer.org/t/use-existing-slicer-modules-with-python-and-cli/2743)

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**Author:** [@hadasara](https://discourse.slicer.org/u/hadasara)\
**Replies:** 5\
**Last updated:** [May 1, 2018, 4:36pm UTC](https://discourse.slicer.org/t/use-existing-slicer-modules-with-python-and-cli/2743 "2018-05-01T16:36:02Z")

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Hi, I followed this tutorial on how to use existing modules in slicer through cli library: It sounds not bad (considering my understanding in cli is close to 0…) Anyway, since I want to use…

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## [Splash screen does not disappear after startup and covers another popup](https://discourse.slicer.org/t/splash-screen-does-not-disappear-after-startup-and-covers-another-popup/2155)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 18\
**Last updated:** [May 1, 2018, 3:49pm UTC](https://discourse.slicer.org/t/splash-screen-does-not-disappear-after-startup-and-covers-another-popup/2155 "2018-05-01T15:49:07Z")

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I just discovered that if Slicer is launched for the first time (ie after removing the settings directory), the splash screen does not disappear after startup, and covers the popup window prompting to accept that Slicer …

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## [Getting coordinates of MRI visible markers](https://discourse.slicer.org/t/getting-coordinates-of-mri-visible-markers/2742)

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**Author:** [@Hanaana](https://discourse.slicer.org/u/Hanaana)\
**Replies:** 1\
**Last updated:** [May 1, 2018, 4:11am UTC](https://discourse.slicer.org/t/getting-coordinates-of-mri-visible-markers/2742 "2018-05-01T04:11:30Z")

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## [Bone segmentation to create 3D-printable STL](https://discourse.slicer.org/t/bone-segmentation-to-create-3d-printable-stl/960)

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**Author:** [@Hanaana](https://discourse.slicer.org/u/Hanaana)\
**Replies:** 20\
**Last updated:** [October 3, 2017, 12:03am UTC](https://discourse.slicer.org/t/bone-segmentation-to-create-3d-printable-stl/960 "2017-10-03T00:03:59Z")

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Hello everyone, I need your support I got this stl as you can see it doesnt look good for further analysis. Can you please tell me how i can modify my stl by modifing my NIfTI data. As i dont know how to edit my st…

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## [Problem with saving segmentation with Fractional Labelmap as Master in Representations](https://discourse.slicer.org/t/problem-with-saving-segmentation-with-fractional-labelmap-as-master-in-representations/2739)

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**Author:** [@trnhx001](https://discourse.slicer.org/u/trnhx001)\
**Replies:** 0\
**Last updated:** [April 30, 2018, 7:11pm UTC](https://discourse.slicer.org/t/problem-with-saving-segmentation-with-fractional-labelmap-as-master-in-representations/2739 "2018-04-30T19:11:31Z")

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Hi everyone, I assigned Fractional labelmap as Master in Representations, so I can have smooth edge when I use Fractional labelmap for Representation in 2D views. However, when I try to save the segmentation with this s…

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## [Atlas-based subcortical nuclei transformation](https://discourse.slicer.org/t/atlas-based-subcortical-nuclei-transformation/2698)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 4\
**Last updated:** [April 30, 2018, 12:47pm UTC](https://discourse.slicer.org/t/atlas-based-subcortical-nuclei-transformation/2698 "2018-04-30T12:47:44Z")

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Hello 3d Slicer forum, I used General Registration (BRAINS) (affine followed by nonrigid B-spline) to align the MNI T1 atlas with a patient’s ac-pc aligned space; the results looked good There are various subcortical n…

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## [SetPosition of ellipsoid](https://discourse.slicer.org/t/setposition-of-ellipsoid/2721)

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**Author:** [@Frederic](https://discourse.slicer.org/u/Frederic)\
**Replies:** 2\
**Last updated:** [April 30, 2018, 12:30pm UTC](https://discourse.slicer.org/t/setposition-of-ellipsoid/2721 "2018-04-30T12:30:43Z")

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Hi all, I have write a little script to draw on slicer an ellipsoid. However, I do not know how to set the position (center), could you please help me? Thanks in advance. The code ellips = vtk.vtkParametricEllipsoi…

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## [Temporal filter fMRI](https://discourse.slicer.org/t/temporal-filter-fmri/2699)

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**Author:** [@Guillaume\_FTN](https://discourse.slicer.org/u/Guillaume_FTN)\
**Replies:** 2\
**Last updated:** [April 30, 2018, 12:25pm UTC](https://discourse.slicer.org/t/temporal-filter-fmri/2699 "2018-04-30T12:25:39Z")

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Operating system: win 10 Slicer version: 4.9 Dear all, Is it possible to make a temporal filter (bandpass) with Slicer ? I have fMRI sequences and I want delete hight and low frequences. Thanks,

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## [Slicer nightly does not build with Qt4/VTK7](https://discourse.slicer.org/t/slicer-nightly-does-not-build-with-qt4-vtk7/2631)

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**Author:** [@Eloise](https://discourse.slicer.org/u/Eloise)\
**Replies:** 14\
**Last updated:** [April 28, 2018, 6:37am UTC](https://discourse.slicer.org/t/slicer-nightly-does-not-build-with-qt4-vtk7/2631 "2018-04-28T06:37:06Z")

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Hello, I am trying to build Slicer (developper mode) on Mac osX running Sierra (version 10.12). I’ve downloaded the latest sources (April 17 2018) with git and I am currently getting this error message below when buildi…

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## [How to save .png as the same name of .mrml while saving](https://discourse.slicer.org/t/how-to-save-png-as-the-same-name-of-mrml-while-saving/2722)

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**Author:** [@thedeadspace8](https://discourse.slicer.org/u/thedeadspace8)\
**Replies:** 1\
**Last updated:** [April 27, 2018, 8:08pm UTC](https://discourse.slicer.org/t/how-to-save-png-as-the-same-name-of-mrml-while-saving/2722 "2018-04-27T20:08:10Z")

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Alright, so I’m new to this software. But I understood how to load a .nii file and then save it. It thankfully saves both in .png and .mrml format (i don’t understand why in .mrml). Anyway, the png file by default saves…

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