# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=384

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

**Page:** 385

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## [Problem with opening .mmrl file](https://discourse.slicer.org/t/problem-with-opening-mmrl-file/7011)

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**Author:** [@sali](https://discourse.slicer.org/u/sali)\
**Replies:** 1\
**Last updated:** [June 3, 2019, 6:24pm UTC](https://discourse.slicer.org/t/problem-with-opening-mmrl-file/7011 "2019-06-03T18:24:50Z")

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Operating system:Mac, windows, linux Slicer version:4.8.0 Expected behavior: Actual behavior: Dear 3D Slicer users I have done segmentation in my CT images and I saved the data in .mmrl files, till two month ago, I …

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## [Problem to import DWI images using Diffusion-weighted DICOM Import (DWIConvert)](https://discourse.slicer.org/t/problem-to-import-dwi-images-using-diffusion-weighted-dicom-import-dwiconvert/6999)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 3\
**Last updated:** [June 3, 2019, 1:55pm UTC](https://discourse.slicer.org/t/problem-to-import-dwi-images-using-diffusion-weighted-dicom-import-dwiconvert/6999 "2019-06-03T13:55:03Z")

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Dears 3DSlicer developers: Specification: Fedora Core 25 (Linux localhost.localdomain 4.8.6-300.fc25.x86\_64) 3DSlicer versions 4.8.1 3DSlicer versions 4.9.0 3DSlicer versions 4.10.0 I have 1768 DWI images (from ep2d\_\_F…

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## [In a create model only see the slices but there are not filling between](https://discourse.slicer.org/t/in-a-create-model-only-see-the-slices-but-there-are-not-filling-between/7008)

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**Author:** [@jose](https://discourse.slicer.org/u/jose)\
**Replies:** 1\
**Last updated:** [June 3, 2019, 10:48am UTC](https://discourse.slicer.org/t/in-a-create-model-only-see-the-slices-but-there-are-not-filling-between/7008 "2019-06-03T10:48:10Z")

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I paint slice by slice in coronal cut using the gradient to do a model of a tooth, but when I make the model only are the slice and not the complete model filling between the slices. Thank you very much!

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## [Ability to grab/selects fiducials depedent on zoom level](https://discourse.slicer.org/t/ability-to-grab-selects-fiducials-depedent-on-zoom-level/6989)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 4\
**Last updated:** [June 2, 2019, 8:42pm UTC](https://discourse.slicer.org/t/ability-to-grab-selects-fiducials-depedent-on-zoom-level/6989 "2019-06-02T20:42:13Z")

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As I was testing the new ruler and orthographic projection bug fixes in the nightly, I noticed that I can’t seem to grab fiducials after they are placed, unless I really zoom in. I have mixed feelings about this. In on…

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## [How can I calculate the total intracranial contents (ICC) volume using 3D slicer modules?](https://discourse.slicer.org/t/how-can-i-calculate-the-total-intracranial-contents-icc-volume-using-3d-slicer-modules/6966)

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**Author:** [@otanit](https://discourse.slicer.org/u/otanit)\
**Replies:** 7\
**Last updated:** [June 1, 2019, 2:55pm UTC](https://discourse.slicer.org/t/how-can-i-calculate-the-total-intracranial-contents-icc-volume-using-3d-slicer-modules/6966 "2019-06-01T14:55:35Z")

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Operating system: Windows 10 Slicer version: Slicer 4.10.1 Expected behavior: Caluculate the total intracranial contents (ICC) volume using 3D slicer modules. Actual behavior: I can’t calculate it in 3D slicer. I wou…

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## [Unable to scroll when loading segmentation](https://discourse.slicer.org/t/unable-to-scroll-when-loading-segmentation/6986)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 1\
**Last updated:** [May 31, 2019, 10:50pm UTC](https://discourse.slicer.org/t/unable-to-scroll-when-loading-segmentation/6986 "2019-05-31T22:50:38Z")

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I see that users loading segmentations without the corresponding image volume get confused, because it is impossible to scroll through the segmentation volume. Is there a good reason to have this behavior?

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## [Bug with Orthographic rendering](https://discourse.slicer.org/t/bug-with-orthographic-rendering/6973)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [May 31, 2019, 10:00pm UTC](https://discourse.slicer.org/t/bug-with-orthographic-rendering/6973 "2019-05-31T22:00:33Z")

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When orthographic rendering is enabled, modifying any of the 3D scene options (box, labels, background etc) resets the field of view (like zoom level). We use orthographic rendering quite a bit to enable the ruler option…

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## [Mapping intensity values to Model Surface as texture?](https://discourse.slicer.org/t/mapping-intensity-values-to-model-surface-as-texture/6972)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 4\
**Last updated:** [May 31, 2019, 11:19am UTC](https://discourse.slicer.org/t/mapping-intensity-values-to-model-surface-as-texture/6972 "2019-05-31T11:19:16Z")

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Is there a way to map the border intensity values of a segmentation to the surface of a model as a texture in 3d slicer to highlight the surfaces dense regions?

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## [Regularization transform is not applied to generated models](https://discourse.slicer.org/t/regularization-transform-is-not-applied-to-generated-models/3448)

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**Author:** [@lukebo](https://discourse.slicer.org/u/lukebo)\
**Replies:** 10\
**Last updated:** [May 30, 2019, 6:49pm UTC](https://discourse.slicer.org/t/regularization-transform-is-not-applied-to-generated-models/3448 "2019-05-30T18:49:36Z")

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Hi everybody, I have CT data which was obtained with a somehow tilted gantry and also with two different slice thicknesses within one series. During the examination of the series in the DICOM-Browser, Slicer notes, tha…

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## [Using the Plus Remote Module from the Python Interactor](https://discourse.slicer.org/t/using-the-plus-remote-module-from-the-python-interactor/6962)

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**Author:** [@fergujm2](https://discourse.slicer.org/u/fergujm2)\
**Replies:** 2\
**Last updated:** [May 30, 2019, 5:46pm UTC](https://discourse.slicer.org/t/using-the-plus-remote-module-from-the-python-interactor/6962 "2019-05-30T17:46:54Z")

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Hi, I am trying to launch a PlusServer instance from the python interactor. Specifically, I need to be able to start/stop the server, and each time I start, I would like to specify the config file. The reason for this…

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## [Scripted Module and editor difference](https://discourse.slicer.org/t/scripted-module-and-editor-difference/6893)

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**Author:** [@prorai](https://discourse.slicer.org/u/prorai)\
**Replies:** 9\
**Last updated:** [May 30, 2019, 1:55pm UTC](https://discourse.slicer.org/t/scripted-module-and-editor-difference/6893 "2019-05-30T13:55:35Z")

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Odd behavior when i run my Scriptable Module and when i run same code in Python interactor. i’m using threshold first to mask the segment and then applying seed grow for making segment, when i run it in python interacto…

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## [Matching two cranial MRIs and quantify translations & rotations between them?](https://discourse.slicer.org/t/matching-two-cranial-mris-and-quantify-translations-rotations-between-them/6961)

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**Author:** [@Michiel](https://discourse.slicer.org/u/Michiel)\
**Replies:** 4\
**Last updated:** [May 30, 2019, 1:20pm UTC](https://discourse.slicer.org/t/matching-two-cranial-mris-and-quantify-translations-rotations-between-them/6961 "2019-05-30T13:20:16Z")

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Hi there! I’m currently trying to match two MRIs of the same patient and quantify both the translations and rotations between the images. They should be (near) perfect matches. I am new to 3D Slicer and I’ve been messi…

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## [Tractography DWI](https://discourse.slicer.org/t/tractography-dwi/6971)

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**Author:** [@pouyahoseini](https://discourse.slicer.org/u/pouyahoseini)\
**Replies:** 1\
**Last updated:** [May 30, 2019, 1:12pm UTC](https://discourse.slicer.org/t/tractography-dwi/6971 "2019-05-30T13:12:06Z")

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Slicer Version : 4.10.1 Hi 3D slicer experts and all I have two group images. DWI and T1 mri. I want to extract fiber bundle from DWI image and merge on T1 image. How can I do that ? Thanks a lot

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## [Coloring voxels in ROI](https://discourse.slicer.org/t/coloring-voxels-in-roi/6956)

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**Author:** [@11124](https://discourse.slicer.org/u/11124)\
**Replies:** 1\
**Last updated:** [May 29, 2019, 11:35am UTC](https://discourse.slicer.org/t/coloring-voxels-in-roi/6956 "2019-05-29T11:35:54Z")

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Hi! I’m writing python plugin for segmentation, using seed growing algorithm. Now, when i found voxels in ROI region, i just set intensity at -1000. Is there any possibility to color ROI voxels?

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## [I can not install 4.8.0 and higher on my computer](https://discourse.slicer.org/t/i-can-not-install-4-8-0-and-higher-on-my-computer/6953)

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**Author:** [@naderinst](https://discourse.slicer.org/u/naderinst)\
**Replies:** 1\
**Last updated:** [May 29, 2019, 3:30am UTC](https://discourse.slicer.org/t/i-can-not-install-4-8-0-and-higher-on-my-computer/6953 "2019-05-29T03:30:30Z")

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Operating system:vista 64 bit Slicer version:4.8.0 Expected behavior: Actual behavior:

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## [Segmentation- Reverting back to Slices](https://discourse.slicer.org/t/segmentation-reverting-back-to-slices/6943)

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**Author:** [@juliawithrow](https://discourse.slicer.org/u/juliawithrow)\
**Replies:** 9\
**Last updated:** [May 28, 2019, 10:34pm UTC](https://discourse.slicer.org/t/segmentation-reverting-back-to-slices/6943 "2019-05-28T22:34:34Z")

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Hi! I’m working on segmenting a skeletal model. I have created the model and saved it, but now want to go back and edit parts of my segmentations in the axial and coronal views, but am not sure how to get back to these …

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## [How to call a function from the logic](https://discourse.slicer.org/t/how-to-call-a-function-from-the-logic/6433)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 3\
**Last updated:** [April 9, 2019, 3:15pm UTC](https://discourse.slicer.org/t/how-to-call-a-function-from-the-logic/6433 "2019-04-09T15:15:56Z")

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Hello, I was wondering how can I call correctly a function that is in the ModuleNameLogic inherited by ScriptedLoadableModuleLogic in python? Currently, I try the following with no success: slicer.modules.moduleName.l…

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## [Is 3D slicer software used for only for human heads or suitable for all human parts?](https://discourse.slicer.org/t/is-3d-slicer-software-used-for-only-for-human-heads-or-suitable-for-all-human-parts/6946)

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**Author:** [@MURUGANANTHAN\_KPRK](https://discourse.slicer.org/u/MURUGANANTHAN_KPRK)\
**Replies:** 1\
**Last updated:** [May 28, 2019, 4:24pm UTC](https://discourse.slicer.org/t/is-3d-slicer-software-used-for-only-for-human-heads-or-suitable-for-all-human-parts/6946 "2019-05-28T16:24:39Z")

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Operating system:windows 7 Slicer version:4.1 Expected behavior:Respected Sir/Madam Whether the 3D slicer software is used for only for human heads or suitable for all human parts? Actual behavior:

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## [Computing transformation matrix on labelmaps](https://discourse.slicer.org/t/computing-transformation-matrix-on-labelmaps/6903)

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**Author:** [@m.hilani](https://discourse.slicer.org/u/m.hilani)\
**Replies:** 2\
**Last updated:** [May 28, 2019, 12:19pm UTC](https://discourse.slicer.org/t/computing-transformation-matrix-on-labelmaps/6903 "2019-05-28T12:19:42Z")

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Hi all, I’ve been working on segmentation of a full body MRI, and after segmenting most of the tissues I realized the need to co-register all the different sequences that I’m using for segmentation. Using 3D slicer, I …

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## [Calculating DVHs for models](https://discourse.slicer.org/t/calculating-dvhs-for-models/6940)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [May 27, 2019, 6:17pm UTC](https://discourse.slicer.org/t/calculating-dvhs-for-models/6940 "2019-05-27T18:17:52Z")

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Slicer version:4.10.1 Hi 3D slicer experts and all Is it possible to calculate DVHs for models( instead of segments ) using Dose Volume Histogram module? Thanks a lot

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## [Slicer release link still at 4.10.1 for Mac](https://discourse.slicer.org/t/slicer-release-link-still-at-4-10-1-for-mac/6937)

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**Author:** [@ljod](https://discourse.slicer.org/u/ljod)\
**Replies:** 4\
**Last updated:** [May 27, 2019, 5:25pm UTC](https://discourse.slicer.org/t/slicer-release-link-still-at-4-10-1-for-mac/6937 "2019-05-27T17:25:48Z")

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Hi! Is this on purpose? Only Linux and Windows have updated links to download the new release here: https://download.slicer.org/ Thanks!

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## [Read pixel data of DICOM RT files](https://discourse.slicer.org/t/read-pixel-data-of-dicom-rt-files/6916)

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**Author:** [@calvin.kohwy](https://discourse.slicer.org/u/calvin.kohwy)\
**Replies:** 5\
**Last updated:** [May 27, 2019, 1:45pm UTC](https://discourse.slicer.org/t/read-pixel-data-of-dicom-rt-files/6916 "2019-05-27T13:45:40Z")

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Slicer version:4.10.2 Dear all Is it possible that we are able to extract the pixel and map it to dose from the dicom files? For example, I have a set of dicom files exported from Treatment planning system (Plan, Str…

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## [X-Ray Phase Contrast Volume Reconstructions  ](https://discourse.slicer.org/t/x-ray-phase-contrast-volume-reconstructions/6596)

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**Author:** [@matdonoghue](https://discourse.slicer.org/u/matdonoghue)\
**Replies:** 5\
**Last updated:** [May 27, 2019, 12:34pm UTC](https://discourse.slicer.org/t/x-ray-phase-contrast-volume-reconstructions/6596 "2019-05-27T12:34:00Z")

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Hi all, I am doing a bit of research in x-ray phase contrast imaging. Part of the research is to demonstrate that this new imaging technique can be used for soft tissue volume reconstruction. The image slices demonstrat…

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## [DTI Brain Mask Including Non-Brain Tissue](https://discourse.slicer.org/t/dti-brain-mask-including-non-brain-tissue/6578)

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**Author:** [@MSpindler](https://discourse.slicer.org/u/MSpindler)\
**Replies:** 33\
**Last updated:** [May 27, 2019, 10:58am UTC](https://discourse.slicer.org/t/dti-brain-mask-including-non-brain-tissue/6578 "2019-05-27T10:58:36Z")

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Dear Slicer community, I’m using slicer 4.10.1. I first converted my nii.gz DWI file to .nrrd using DWIConvert. After that, I create a brain mask using “Diffusion Brain Masking”. But the resulting mask includes a lot o…

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## [Why the "slicerDMRI" module can not find in latest version(4.10.2)](https://discourse.slicer.org/t/why-the-slicerdmri-module-can-not-find-in-latest-version-4-10-2/6895)

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**Author:** [@Jin](https://discourse.slicer.org/u/Jin)\
**Replies:** 7\
**Last updated:** [May 27, 2019, 10:57am UTC](https://discourse.slicer.org/t/why-the-slicerdmri-module-can-not-find-in-latest-version-4-10-2/6895 "2019-05-27T10:57:52Z")

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why the “slicerDMRI” module can not find in latest version(4.10.2), thanks! I can not get the DTI volume and tractography?

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## [Changing image display between 4.10.x and 4.8.x using the same Window level and lookup table ?](https://discourse.slicer.org/t/changing-image-display-between-4-10-x-and-4-8-x-using-the-same-window-level-and-lookup-table/6842)

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**Author:** [@runze](https://discourse.slicer.org/u/runze)\
**Replies:** 3\
**Last updated:** [May 26, 2019, 5:55pm UTC](https://discourse.slicer.org/t/changing-image-display-between-4-10-x-and-4-8-x-using-the-same-window-level-and-lookup-table/6842 "2019-05-26T17:55:11Z")

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I used 4.8.1 and started to use 4.10.1 recently. I found that they showed the same image in different gray levels. I have the same window level and lookup table settings. The data was loaded through PETDICOMextension…

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## [How to hard the transform for stl?](https://discourse.slicer.org/t/how-to-hard-the-transform-for-stl/6929)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 3\
**Last updated:** [May 26, 2019, 11:49am UTC](https://discourse.slicer.org/t/how-to-hard-the-transform-for-stl/6929 "2019-05-26T11:49:01Z")

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\[1, 0, 0, 2\], \[0, 1, 0, 2\], \[0, 0, 1, 2\], \[0, 0, 0, 0.01\] the “0.01” seems not work in slicer and cannot save as well as.

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## [Please add cropping and padding options to maskVolume effect in ExtraEffect tools](https://discourse.slicer.org/t/please-add-cropping-and-padding-options-to-maskvolume-effect-in-extraeffect-tools/6691)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [May 25, 2019, 10:05pm UTC](https://discourse.slicer.org/t/please-add-cropping-and-padding-options-to-maskvolume-effect-in-extraeffect-tools/6691 "2019-05-25T22:05:38Z")

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It is common in our field to stuff whole bunch of genetically samples into the same scan to cut down the scanning costs/time (eg 10-15 zebrafish from the same clutch). We are training our folks to use Slicer to do a qui…

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## [I cannot change the window/center level with left click](https://discourse.slicer.org/t/i-cannot-change-the-window-center-level-with-left-click/6923)

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**Author:** [@ecgt](https://discourse.slicer.org/u/ecgt)\
**Replies:** 1\
**Last updated:** [May 25, 2019, 2:20am UTC](https://discourse.slicer.org/t/i-cannot-change-the-window-center-level-with-left-click/6923 "2019-05-25T02:20:39Z")

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Problem report for Slicer 4.11.0-2019-05-01 win-amd64: Change window level does not work

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## [Save DWI trace as separate stacks according to b value](https://discourse.slicer.org/t/save-dwi-trace-as-separate-stacks-according-to-b-value/6920)

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**Author:** [@aikast](https://discourse.slicer.org/u/aikast)\
**Replies:** 0\
**Last updated:** [May 24, 2019, 8:23pm UTC](https://discourse.slicer.org/t/save-dwi-trace-as-separate-stacks-according-to-b-value/6920 "2019-05-24T20:23:06Z")

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I used MultiVolumeExplorer to separate DWI trace images based on b values as separate stacks but can I save those (e.g. b0 stack and b1000 stack) as separate .nrrd files?

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