# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=268

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

**Page:** 269

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## [Problem starting Slicer](https://discourse.slicer.org/t/problem-starting-slicer/18913)

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**Author:** [@german\_91](https://discourse.slicer.org/u/german_91)\
**Replies:** 3\
**Last updated:** [July 25, 2021, 2:00pm UTC](https://discourse.slicer.org/t/problem-starting-slicer/18913 "2021-07-25T14:00:02Z")

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Hi Community, I’m getting into the software. I have a problem with the software when starting, the window is blank, I tried downloading the 2 versions for windows, the Stable Release version and the Preview Release versi…

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## [Is it possible to fill in all black outside the segmentation?](https://discourse.slicer.org/t/is-it-possible-to-fill-in-all-black-outside-the-segmentation/18914)

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**Author:** [@angelsosamd](https://discourse.slicer.org/u/angelsosamd)\
**Replies:** 2\
**Last updated:** [July 25, 2021, 12:26pm UTC](https://discourse.slicer.org/t/is-it-possible-to-fill-in-all-black-outside-the-segmentation/18914 "2021-07-25T12:26:41Z")

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Hi! Is it possible to fill in all black outside the segmentation? (background) Regards, Angel S.

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## [Decomposing the Transformation matrix and the order of operation?](https://discourse.slicer.org/t/decomposing-the-transformation-matrix-and-the-order-of-operation/18904)

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**Author:** [@Amit\_1993](https://discourse.slicer.org/u/Amit_1993)\
**Replies:** 1\
**Last updated:** [July 24, 2021, 12:27pm UTC](https://discourse.slicer.org/t/decomposing-the-transformation-matrix-and-the-order-of-operation/18904 "2021-07-24T12:27:47Z")

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Hi all! In 3D slicer Image Registration Operation : I want to decompose the individual Transformation operation as a product of Translation Matrix, Scaling Matrix, and Rotation Matrix(if used). So, I need to know the o…

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## [Problem with volumetric mesh](https://discourse.slicer.org/t/problem-with-volumetric-mesh/18881)

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**Author:** [@rcapozza](https://discourse.slicer.org/u/rcapozza)\
**Replies:** 5\
**Last updated:** [July 23, 2021, 5:03pm UTC](https://discourse.slicer.org/t/problem-with-volumetric-mesh/18881 "2021-07-23T17:03:50Z")

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Hi guys. I’ve a series of ct-scans images of a central part of human tibia, this was obtained with a Stratec pQCT machine and exported in jpg format, named accordingly, for perform later import in Slicer software. Once …

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## [When I manually change my Transformation Matrix, I am Having some problem. I want to know the logic or reason behind it. know the logic ](https://discourse.slicer.org/t/when-i-manually-change-my-transformation-matrix-i-am-having-some-problem-i-want-to-know-the-logic-or-reason-behind-it-know-the-logic/18894)

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**Author:** [@Amit\_1993](https://discourse.slicer.org/u/Amit_1993)\
**Replies:** 1\
**Last updated:** [July 23, 2021, 4:05pm UTC](https://discourse.slicer.org/t/when-i-manually-change-my-transformation-matrix-i-am-having-some-problem-i-want-to-know-the-logic-or-reason-behind-it-know-the-logic/18894 "2021-07-23T16:05:11Z")

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I have two images, one is CT image and another one is a functional image (SPECT). First to align the center of both images I have manually adjusted the transformation matrix. Then I want to do the scaling so that I have…

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## [The Input and Output option is not showing up for the slicer morph extension](https://discourse.slicer.org/t/the-input-and-output-option-is-not-showing-up-for-the-slicer-morph-extension/18888)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 1\
**Last updated:** [July 23, 2021, 3:45pm UTC](https://discourse.slicer.org/t/the-input-and-output-option-is-not-showing-up-for-the-slicer-morph-extension/18888 "2021-07-23T15:45:34Z")

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Dear all, I downloaded the slicer morph extension to use the \_rec.log file for the reconstruction. however, the input and output option did not show up on my program and I was unable to use the log file. I tried redow…

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## [Add number of extension installations to extension manager](https://discourse.slicer.org/t/add-number-of-extension-installations-to-extension-manager/18847)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 21\
**Last updated:** [July 23, 2021, 11:43am UTC](https://discourse.slicer.org/t/add-number-of-extension-installations-to-extension-manager/18847 "2021-07-23T11:43:17Z")

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In extension manager when a user installs an extension, it would be nice to add a counter that tracks the number of installations e.g. next to the stars vote. It would be nice if the counter also tracks other dependant …

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## [An issue when open DICOM images](https://discourse.slicer.org/t/an-issue-when-open-dicom-images/15029)

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**Author:** [@Magdy](https://discourse.slicer.org/u/Magdy)\
**Replies:** 1\
**Last updated:** [July 22, 2021, 9:36pm UTC](https://discourse.slicer.org/t/an-issue-when-open-dicom-images/15029 "2021-07-22T21:36:31Z")

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Hi Colleagues, Whenever I try to open dicom PET images, the following error persists: Traceback (most recent call last): File “D:\\Progam Files\\Slicer 4.10.2\\lib\\Slicer-4.10\\qt-scripted-modules\\DICOMLib\\DICOMWidgets.py…

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## [2D phase contrast MRI](https://discourse.slicer.org/t/2d-phase-contrast-mri/18876)

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**Author:** [@Hamed](https://discourse.slicer.org/u/Hamed)\
**Replies:** 1\
**Last updated:** [July 22, 2021, 9:16pm UTC](https://discourse.slicer.org/t/2d-phase-contrast-mri/18876 "2021-07-22T21:16:08Z")

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Hi, Is it possible to read and analyse 2D phase contrast MRI images in 3D Slicer? Many thanks in advance.

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## [new extension guide](https://discourse.slicer.org/t/new-extension-guide/18863)

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**Author:** [@shatz](https://discourse.slicer.org/u/shatz)\
**Replies:** 1\
**Last updated:** [July 21, 2021, 3:58pm UTC](https://discourse.slicer.org/t/new-extension-guide/18863 "2021-07-21T15:58:24Z")

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Is there any easy guide out there for a python dev to begin work on a new extension idea? Im very new to this slicer stuff and would like to make a new one. I would like a very basic template that I can start with, I wi…

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## [Resolution of CT images](https://discourse.slicer.org/t/resolution-of-ct-images/18857)

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**Author:** [@Mohammed110](https://discourse.slicer.org/u/Mohammed110)\
**Replies:** 3\
**Last updated:** [July 21, 2021, 1:23pm UTC](https://discourse.slicer.org/t/resolution-of-ct-images/18857 "2021-07-21T13:23:20Z")

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Dear all, I have CT images obtained online and I want to know the resolution and slice thickness, is that possible, I would appreciate any help Thanks Mo

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## [Mask Shifting in Segment Editor](https://discourse.slicer.org/t/mask-shifting-in-segment-editor/18850)

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**Author:** [@Esteban\_Barreiro](https://discourse.slicer.org/u/Esteban_Barreiro)\
**Replies:** 1\
**Last updated:** [July 21, 2021, 11:56am UTC](https://discourse.slicer.org/t/mask-shifting-in-segment-editor/18850 "2021-07-21T11:56:24Z")

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Hi everybody! hope you are ok. I found that sometimes masks from the Segment Editor shift before zoom in or out in Axial, Sagital and Coronal views. Center the views (even with axial,sagital and coronal views linked) do…

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## [MRI CT Registration](https://discourse.slicer.org/t/mri-ct-registration/18843)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 3\
**Last updated:** [July 21, 2021, 2:02am UTC](https://discourse.slicer.org/t/mri-ct-registration/18843 "2021-07-21T02:02:33Z")

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Hello, I have tried a few techniques to register pelvic bones rigidly from MRI to CT image of one patient. For all I put the CT as the fixed image. First tried Mutual Information registration with cropping the dark are…

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## [Mirroring a model](https://discourse.slicer.org/t/mirroring-a-model/18059)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [July 21, 2021, 1:37am UTC](https://discourse.slicer.org/t/mirroring-a-model/18059 "2021-07-21T01:37:35Z")

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i have this case of facia asymmertry , my purpose is to evaluatr zygoma position steps i followed 1 segment the skull 2 segment zygoma 3 trnasform zygoma to model 4 mirrror zygoma around x axis in suface model/ adva…

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## [How to segment brain part and save segmentation and 3D image as one file not separate file? ](https://discourse.slicer.org/t/how-to-segment-brain-part-and-save-segmentation-and-3d-image-as-one-file-not-separate-file/18064)

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**Author:** [@abhijeet2410](https://discourse.slicer.org/u/abhijeet2410)\
**Replies:** 1\
**Last updated:** [July 21, 2021, 1:33am UTC](https://discourse.slicer.org/t/how-to-segment-brain-part-and-save-segmentation-and-3d-image-as-one-file-not-separate-file/18064 "2021-07-21T01:33:30Z")

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Hello Team, Greetings!! Thank you very much for best service. I have two question this time: How to remove skull part from the 3 D brain image (I am focusing on 3D part only). For my project, I want (segmentation…

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## [Export 3D image partial opacity](https://discourse.slicer.org/t/export-3d-image-partial-opacity/18816)

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**Author:** [@Chuns\_SS](https://discourse.slicer.org/u/Chuns_SS)\
**Replies:** 8\
**Last updated:** [July 21, 2021, 1:13am UTC](https://discourse.slicer.org/t/export-3d-image-partial-opacity/18816 "2021-07-21T01:13:04Z")

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Hi is there a way to export a 3D image with reduced opacity?

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## [Slicer on a Surface Hub 2S](https://discourse.slicer.org/t/slicer-on-a-surface-hub-2s/18844)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 3\
**Last updated:** [July 21, 2021, 12:17am UTC](https://discourse.slicer.org/t/slicer-on-a-surface-hub-2s/18844 "2021-07-21T00:17:45Z")

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I know you can run Slicer on a Surface Tablet and a Surface Studio, but has anyone tried on a Surface Hub 2S?

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## [Export DICOM as tif 16bit problems](https://discourse.slicer.org/t/export-dicom-as-tif-16bit-problems/18824)

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**Author:** [@ibl3d](https://discourse.slicer.org/u/ibl3d)\
**Replies:** 6\
**Last updated:** [July 20, 2021, 10:11pm UTC](https://discourse.slicer.org/t/export-dicom-as-tif-16bit-problems/18824 "2021-07-20T22:11:40Z")

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Hello everyone, I wanted to comment on a couple of problems How can I export a serie of DICOM files to a serie of individual 16b tif files. When I try it I get a multi-image TIFF with broken levels. When I try to expo…

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## [VolumeReconstruction module: how can the output volume be saved?](https://discourse.slicer.org/t/volumereconstruction-module-how-can-the-output-volume-be-saved/18121)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 15\
**Last updated:** [July 20, 2021, 7:43pm UTC](https://discourse.slicer.org/t/volumereconstruction-module-how-can-the-output-volume-be-saved/18121 "2021-07-20T19:43:50Z")

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Operating system: Win64 Slicer version: Slicer 4.11.20210226 Expected behavior: Build and save ultrasound volume through module VolumeReconstruction Actual behavior: The expected output volume is always empty. Hell…

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## [export in single fscv file](https://discourse.slicer.org/t/export-in-single-fscv-file/18823)

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**Author:** [@Kever\_L](https://discourse.slicer.org/u/Kever_L)\
**Replies:** 1\
**Last updated:** [July 20, 2021, 7:40pm UTC](https://discourse.slicer.org/t/export-in-single-fscv-file/18823 "2021-07-20T19:40:55Z")

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Operating system: Windows 10 Slicer version:4.11.20210226 r29738 Expected behavior: export all curves + fiducial in a single .fcsv Actual behavior: only possible to save curves individually in several .fscv Hello, I…

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## [Iterating through segments in a segmentation Node](https://discourse.slicer.org/t/iterating-through-segments-in-a-segmentation-node/18802)

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**Author:** [@Griffin](https://discourse.slicer.org/u/Griffin)\
**Replies:** 6\
**Last updated:** [July 20, 2021, 6:51pm UTC](https://discourse.slicer.org/t/iterating-through-segments-in-a-segmentation-node/18802 "2021-07-20T18:51:20Z")

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I know this has got to be something obvious that I’m not getting but I’ve spent a really long time longer for the answer and I can’t seem to find it. If I have a segmentation node loaded in and saved as a variable, how c…

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## [How do figure out superficial area of the green part which is covered by red?](https://discourse.slicer.org/t/how-do-figure-out-superficial-area-of-the-green-part-which-is-covered-by-red/18612)

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**Author:** [@QSX747](https://discourse.slicer.org/u/QSX747)\
**Replies:** 7\
**Last updated:** [July 20, 2021, 11:41am UTC](https://discourse.slicer.org/t/how-do-figure-out-superficial-area-of-the-green-part-which-is-covered-by-red/18612 "2021-07-20T11:41:11Z")

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Hi! Based on the preoperative MRI, I am trying to reconstruct the sellar region tumor( green part) and the surrounding peritumor capsule( red part) by using 3Dslicer, and try to calculate the coverage of the sellar d…

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## [Copy 2D Markups Plane for other slices in CTP](https://discourse.slicer.org/t/copy-2d-markups-plane-for-other-slices-in-ctp/18770)

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**Author:** [@Dhruba](https://discourse.slicer.org/u/Dhruba)\
**Replies:** 8\
**Last updated:** [July 19, 2021, 6:33pm UTC](https://discourse.slicer.org/t/copy-2d-markups-plane-for-other-slices-in-ctp/18770 "2021-07-19T18:33:23Z")

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Hello, I am trying to annotate my CTP data using Markups Plane. There are a total of 158 slices in my CT data. I want to create Markup Plane in only 1 slice and copy the markup for 3 slices above and 3 slices below of th…

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## [Isotropic voxel head CT](https://discourse.slicer.org/t/isotropic-voxel-head-ct/18741)

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**Author:** [@LittleTchat](https://discourse.slicer.org/u/LittleTchat)\
**Replies:** 2\
**Last updated:** [July 19, 2021, 3:08pm UTC](https://discourse.slicer.org/t/isotropic-voxel-head-ct/18741 "2021-07-19T15:08:52Z")

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Operating system: MacOS Catalina Slicer version: 4.11 Hi ! I’m new to Slicer and Python, so I apologize in advance if my question has already been asking or if it’s not clear. I’m working with 124 head CTs. The segment…

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## [Set Volume Rendering Options with PYTHON](https://discourse.slicer.org/t/set-volume-rendering-options-with-python/18783)

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**Author:** [@Jonathan\_Lesage](https://discourse.slicer.org/u/Jonathan_Lesage)\
**Replies:** 1\
**Last updated:** [July 19, 2021, 2:02pm UTC](https://discourse.slicer.org/t/set-volume-rendering-options-with-python/18783 "2021-07-19T14:02:15Z")

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Hello, I have seen some posts and scripts in the repository for setting parameters for volume rendering, however, I cannot seem to find a way to set the Synchronize with Volumes Module and set the Scalar Opacity Mapping…

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## [Wrong output volume using Model to LabelMap](https://discourse.slicer.org/t/wrong-output-volume-using-model-to-labelmap/18750)

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**Author:** [@jean-marie\_bonny](https://discourse.slicer.org/u/jean-marie_bonny)\
**Replies:** 3\
**Last updated:** [July 19, 2021, 1:44pm UTC](https://discourse.slicer.org/t/wrong-output-volume-using-model-to-labelmap/18750 "2021-07-19T13:44:44Z")

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Dear 3D slicer community I have a question relating to the Model to labelmap module. I generated a .vtp model with the RATS software. Under 3dslicer, the model looks correct and the segmentation overlaps well with the i…

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## [Transform Module](https://discourse.slicer.org/t/transform-module/18667)

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**Author:** [@reddington.15](https://discourse.slicer.org/u/reddington.15)\
**Replies:** 3\
**Last updated:** [July 19, 2021, 11:44am UTC](https://discourse.slicer.org/t/transform-module/18667 "2021-07-19T11:44:41Z")

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Hello, In a brief synopsis I am trying to calculate the deformation of the pelvis from a pre and post CT scan after impact testing. Once I segment both pelvis bones out using segmentation editor and wrap solidfy, I alig…

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## [Breach warning, Open Sound Control, test with Pure Data errors](https://discourse.slicer.org/t/breach-warning-open-sound-control-test-with-pure-data-errors/5045)

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**Author:** [@jadam1995](https://discourse.slicer.org/u/jadam1995)\
**Replies:** 1\
**Last updated:** [June 23, 2019, 1:55pm UTC](https://discourse.slicer.org/t/breach-warning-open-sound-control-test-with-pure-data-errors/5045 "2019-06-23T13:55:27Z")

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Operating system: Windows (6.1.7601) Slicer version: 4.10.0 I am trying to run the Breach Warning and Sound Navigation modules in 3d Slicer. I have followed all of the appropriate steps to install the IGT, Sound Contro…

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## [Problems with SkyscanRecomimport](https://discourse.slicer.org/t/problems-with-skyscanrecomimport/18785)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 2\
**Last updated:** [July 18, 2021, 5:12pm UTC](https://discourse.slicer.org/t/problems-with-skyscanrecomimport/18785 "2021-07-18T17:12:31Z")

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Dear all, I am trying to reconstruct the CT images, but it is not working. I used Skyscan 1272 to achieve the CT data and they are in tiff format. When I plugged in the tiff data into Volume Rendering or Image Stack, …

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## [Perform cortical and  trabecular bone segmentation of a Talus bone to generate a 2body STL file](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950)

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**Author:** [@Manav\_Kothari](https://discourse.slicer.org/u/Manav_Kothari)\
**Replies:** 2\
**Last updated:** [July 18, 2021, 3:15am UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950 "2021-07-18T03:15:22Z")

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I apologise for being extremely naive in the field of biomechanics and radiology but I need to extract a 3D model of Talus bone from a CT scan of a foot. So far I have been successful in segmenting the outer structure of…

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