# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=425

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

**Page:** 426

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## [What is the default co-ordinate system in nrrd files saved from Slicer?   ](https://discourse.slicer.org/t/what-is-the-default-co-ordinate-system-in-nrrd-files-saved-from-slicer/2719)

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**Author:** [@Krishna\_Nanda](https://discourse.slicer.org/u/Krishna_Nanda)\
**Replies:** 1\
**Last updated:** [April 27, 2018, 3:33pm UTC](https://discourse.slicer.org/t/what-is-the-default-co-ordinate-system-in-nrrd-files-saved-from-slicer/2719 "2018-04-27T15:33:43Z")

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Operating system: Windows 7 Slicer version: 4.8.0 Expected behavior: Actual behavior: Hello, I have a quick question about the nrrd files saved from Slicer. Is the default nrrd co-ordinate system LPS? When and how c…

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## [Segmentation according to a chosen midsagittal plane](https://discourse.slicer.org/t/segmentation-according-to-a-chosen-midsagittal-plane/2596)

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**Author:** [@Arnaud](https://discourse.slicer.org/u/Arnaud)\
**Replies:** 2\
**Last updated:** [April 27, 2018, 9:50am UTC](https://discourse.slicer.org/t/segmentation-according-to-a-chosen-midsagittal-plane/2596 "2018-04-27T09:50:14Z")

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hi everyone, I’m working on surgical planning in facial bone repositioning. I’m focusing actually on broken zygomatic bones. To plane the repositioning I use the mirroring of the normal side. (considering that the pati…

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## [fluorescent data extraction](https://discourse.slicer.org/t/fluorescent-data-extraction/2705)

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**Author:** [@FungalSlicer](https://discourse.slicer.org/u/FungalSlicer)\
**Replies:** 4\
**Last updated:** [April 27, 2018, 9:31am UTC](https://discourse.slicer.org/t/fluorescent-data-extraction/2705 "2018-04-27T09:31:38Z")

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Hey guys, I am looking for a way to extract data from stacked fluorescent image data of specific tip-growing fungi. I already remodeled the surface and reduced it to a centerline (which i managed to load into 3Dslicer a…

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## [Pre-build or Locally-build 3dSlicer under Ubuntu 16.04 does NOT start: Failed to obtain launcher executable name!](https://discourse.slicer.org/t/pre-build-or-locally-build-3dslicer-under-ubuntu-16-04-does-not-start-failed-to-obtain-launcher-executable-name/2322)

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**Author:** [@MGM](https://discourse.slicer.org/u/MGM)\
**Replies:** 10\
**Last updated:** [April 27, 2018, 8:09am UTC](https://discourse.slicer.org/t/pre-build-or-locally-build-3dslicer-under-ubuntu-16-04-does-not-start-failed-to-obtain-launcher-executable-name/2322 "2018-04-27T08:09:17Z")

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Hi everyone, I tried to build 3dSlicer under Ubuntu 16.04, following all steps here But, still can’t find how to run it ? Please, anyone, have a simple instruction to make it running? Thanks

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## [How to split 4D volumes to individual 3D volumes?](https://discourse.slicer.org/t/how-to-split-4d-volumes-to-individual-3d-volumes/2707)

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**Author:** [@xuec](https://discourse.slicer.org/u/xuec)\
**Replies:** 5\
**Last updated:** [April 27, 2018, 6:53am UTC](https://discourse.slicer.org/t/how-to-split-4d-volumes-to-individual-3d-volumes/2707 "2018-04-27T06:53:32Z")

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## [2d to 3D registration of MRI to pathology](https://discourse.slicer.org/t/2d-to-3d-registration-of-mri-to-pathology/2708)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 1\
**Last updated:** [April 26, 2018, 7:42pm UTC](https://discourse.slicer.org/t/2d-to-3d-registration-of-mri-to-pathology/2708 "2018-04-26T19:42:26Z")

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I am working on that is looking at pathology of resected aneurysms and comparing with an MRI image sequence. Currently the plan is to analyze each image in 4 quadrants so accuracy doesn’t have be exact, (in the future a…

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## [is there any ways to save transformation matrix using command line?](https://discourse.slicer.org/t/is-there-any-ways-to-save-transformation-matrix-using-command-line/2647)

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**Author:** [@xuec](https://discourse.slicer.org/u/xuec)\
**Replies:** 2\
**Last updated:** [April 23, 2018, 1:37pm UTC](https://discourse.slicer.org/t/is-there-any-ways-to-save-transformation-matrix-using-command-line/2647 "2018-04-23T13:37:22Z")

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Operating system:Windows 7 Slicer version:4.2.2 I am doing BRAINSDemonWrap (command line), however I cannot find any output for transformation matrix, any suggestions how I could save the transformation matrix please? …

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## [How export DICOM](https://discourse.slicer.org/t/how-export-dicom/2690)

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**Author:** [@mukatyz](https://discourse.slicer.org/u/mukatyz)\
**Replies:** 2\
**Last updated:** [April 25, 2018, 7:27pm UTC](https://discourse.slicer.org/t/how-export-dicom/2690 "2018-04-25T19:27:08Z")

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Hello, How can i compress a serie of images in a volume 3d from create DICOM series module. Thank

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## [Slicer building error on Windows 10](https://discourse.slicer.org/t/slicer-building-error-on-windows-10/2692)

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**Author:** [@wpgao](https://discourse.slicer.org/u/wpgao)\
**Replies:** 0\
**Last updated:** [April 26, 2018, 6:42am UTC](https://discourse.slicer.org/t/slicer-building-error-on-windows-10/2692 "2018-04-26T06:42:07Z")

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Hi guys, Recently, I builded Slicer on Window 10 with qt 4.8.7 and got following error. Slicer\\Libs\\vtkSegmentationCore\\vtkBinaryLabelmapToClosedSurfaceConversionRule.cxx(28): fatal error C1083: Cannot open include fil…

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## [Compress/Compact single image files .dcm into a volume.](https://discourse.slicer.org/t/compress-compact-single-image-files-dcm-into-a-volume/2691)

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**Author:** [@ANDREY\_FELIPE\_ARANGO](https://discourse.slicer.org/u/ANDREY_FELIPE_ARANGO)\
**Replies:** 0\
**Last updated:** [April 26, 2018, 3:11am UTC](https://discourse.slicer.org/t/compress-compact-single-image-files-dcm-into-a-volume/2691 "2018-04-26T03:11:18Z")

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Hi everyone, how can I create a volume compacting images .dcm after running CLI module “Create a Dicom Series” in Python?

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## [fragmental bone](https://discourse.slicer.org/t/fragmental-bone/2689)

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**Author:** [@Patrycja\_Grygny](https://discourse.slicer.org/u/Patrycja_Grygny)\
**Replies:** 1\
**Last updated:** [April 25, 2018, 6:54pm UTC](https://discourse.slicer.org/t/fragmental-bone/2689 "2018-04-25T18:54:58Z")

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Operating system: MacOS Slicer version: 4.8.1 Expected behavior: Actual behavior: Hi, I have a cremation material which is located in the Popiel during the Pomeranian culture period. Itry to crop a fragments and do …

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## [Delete fibers manually](https://discourse.slicer.org/t/delete-fibers-manually/2672)

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**Author:** [@mali](https://discourse.slicer.org/u/mali)\
**Replies:** 0\
**Last updated:** [April 24, 2018, 12:59pm UTC](https://discourse.slicer.org/t/delete-fibers-manually/2672 "2018-04-24T12:59:46Z")

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Dear all, after tractography I tried to delete some of the fibers manually but unfortunately the delete option in Tractography Display does not work even though I enabled the interactive edit. Could you give me some adv…

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## [Diffusion Tensor Estimation is not working with my data](https://discourse.slicer.org/t/diffusion-tensor-estimation-is-not-working-with-my-data/2588)

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**Author:** [@mali](https://discourse.slicer.org/u/mali)\
**Replies:** 5\
**Last updated:** [April 23, 2018, 7:59pm UTC](https://discourse.slicer.org/t/diffusion-tensor-estimation-is-not-working-with-my-data/2588 "2018-04-23T19:59:44Z")

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Hello everyone, I hope some of you can help me with my problem. My diffusion scans (Siemens) have the volume type MRMLMulti. I used the ResampleScalar/Vector/DWI Volume command to get a DWI output and I can see its diff…

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## [Error after installing radiomics](https://discourse.slicer.org/t/error-after-installing-radiomics/2668)

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**Author:** [@Diana](https://discourse.slicer.org/u/Diana)\
**Replies:** 3\
**Last updated:** [April 23, 2018, 4:16pm UTC](https://discourse.slicer.org/t/error-after-installing-radiomics/2668 "2018-04-23T16:16:19Z")

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Hello, everytime I try to run Slicer 3D an error table shows up it started after I installed Radiomics, which I had to do offline from a file(downloaded from https://slicer.kitware.com/midas3/download/index?items=3528…

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## [App crashing on windows server](https://discourse.slicer.org/t/app-crashing-on-windows-server/2659)

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**Author:** [@anandmulay3](https://discourse.slicer.org/u/anandmulay3)\
**Replies:** 2\
**Last updated:** [April 23, 2018, 1:25pm UTC](https://discourse.slicer.org/t/app-crashing-on-windows-server/2659 "2018-04-23T13:25:02Z")

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OS : windows server 2016 standard app is not working on this windows 10 (windows server 2016) version. Does it have any issue for this OS support.

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## [Volume Cropping in Python Script](https://discourse.slicer.org/t/volume-cropping-in-python-script/2585)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 8\
**Last updated:** [April 23, 2018, 5:08am UTC](https://discourse.slicer.org/t/volume-cropping-in-python-script/2585 "2018-04-23T05:08:46Z")

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Dear all, I just checked Python\_scripting and ScriptRepository pages and couldn’t find an example for cropping an image, I wrote this simple example. It runs without problem inside a module or extension but when I run i…

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## [Gen Registration (Brains) fails despite overlap of series](https://discourse.slicer.org/t/gen-registration-brains-fails-despite-overlap-of-series/2644)

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**Author:** [@alex](https://discourse.slicer.org/u/alex)\
**Replies:** 11\
**Last updated:** [April 23, 2018, 2:33am UTC](https://discourse.slicer.org/t/gen-registration-brains-fails-despite-overlap-of-series/2644 "2018-04-23T02:33:28Z")

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Dear Slicer community, My apologies for posting this again as new Topic. I had initially added that to a discussion from July 2017 initiated by Rewati K but then realized that this discussion was marked as solved… by no…

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## [Visual regression in Volume Rendering](https://discourse.slicer.org/t/visual-regression-in-volume-rendering/2658)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [April 22, 2018, 12:39pm UTC](https://discourse.slicer.org/t/visual-regression-in-volume-rendering/2658 "2018-04-22T12:39:23Z")

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Today’s build has introduced a visual regression while rotating a 3D model in Volume rendering. A new VTK commit has been pulled in. It seems to request a too high frame rate. Please see two screen video shots with Slice…

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## [OpenIGTLink module receiving data from the sensor](https://discourse.slicer.org/t/openigtlink-module-receiving-data-from-the-sensor/2577)

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**Author:** [@wpgao](https://discourse.slicer.org/u/wpgao)\
**Replies:** 8\
**Last updated:** [April 21, 2018, 9:54am UTC](https://discourse.slicer.org/t/openigtlink-module-receiving-data-from-the-sensor/2577 "2018-04-21T09:54:49Z")

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Hi all, How to obtain the message with a complicate data structure, such as head info plus two 4x4 matrices, sent from the sensor via network using openIGTLink? Many thanks! Operating system: win 7 Slicer version: 4.…

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## [General registration (BRAINS) returns "Joint PDF summed to zero" error](https://discourse.slicer.org/t/general-registration-brains-returns-joint-pdf-summed-to-zero-error/684)

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**Author:** [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Replies:** 7\
**Last updated:** [July 13, 2017, 6:43pm UTC](https://discourse.slicer.org/t/general-registration-brains-returns-joint-pdf-summed-to-zero-error/684 "2017-07-13T18:43:07Z")

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Operating system: Mac OSX 10.9.5 Slicer version: 4.7 I am trying to run a registration in the BRAINS module, that is somewhat unique and different from the sample cases given online. I have a grayscale FA scalar volume…

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## [How to remove an organ (Hands or foot) in DICOM Image of Phantom with 3D Slicer](https://discourse.slicer.org/t/how-to-remove-an-organ-hands-or-foot-in-dicom-image-of-phantom-with-3d-slicer/2633)

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**Author:** [@MeryMB](https://discourse.slicer.org/u/MeryMB)\
**Replies:** 4\
**Last updated:** [April 19, 2018, 5:48pm UTC](https://discourse.slicer.org/t/how-to-remove-an-organ-hands-or-foot-in-dicom-image-of-phantom-with-3d-slicer/2633 "2018-04-19T17:48:53Z")

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Dear Slicer User Good day I am a beginner with Slicer I Produce DICOM image of XCAT and I want to use them in TPS for breast cancer Radiation therapy. I have to remove its left hand before planning because it is on b…

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## [Analysis with SPHARM-PDM](https://discourse.slicer.org/t/analysis-with-spharm-pdm/2518)

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**Author:** [@Pilar](https://discourse.slicer.org/u/Pilar)\
**Replies:** 4\
**Last updated:** [April 19, 2018, 4:07pm UTC](https://discourse.slicer.org/t/analysis-with-spharm-pdm/2518 "2018-04-19T16:07:51Z")

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Hi 3D-Slicer users, I am having problems using the SPHARM-PDM module. I read the user tutorial (May 2017) but when I apply the module, the status says completed with errors. The purpose of my PhD is to make the compari…

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## [Exporting models for surgical navigation](https://discourse.slicer.org/t/exporting-models-for-surgical-navigation/840)

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**Author:** [@drpreezy](https://discourse.slicer.org/u/drpreezy)\
**Replies:** 6\
**Last updated:** [August 17, 2017, 6:41am UTC](https://discourse.slicer.org/t/exporting-models-for-surgical-navigation/840 "2017-08-17T06:41:44Z")

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Operating system: WINDOWS Slicer version:4.6.2 Expected behavior: First and foremost, thank you for the outstanding work with 3DSlicer, it has been very useful in my research. I am currently taking DICOM data from CT…

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## [ROI to IJK coordinates](https://discourse.slicer.org/t/roi-to-ijk-coordinates/2589)

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**Author:** [@zjx1805](https://discourse.slicer.org/u/zjx1805)\
**Replies:** 13\
**Last updated:** [April 19, 2018, 1:04pm UTC](https://discourse.slicer.org/t/roi-to-ijk-coordinates/2589 "2018-04-19T13:04:25Z")

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I am trying to get iMin, iMax, jMin, jMax, kMin, kMax from some ROI node using Python script such that croppedVolume = dataVolume\[kMin:kMax, jMin:jMax, iMin:iMax\] and then I will perform some analysis on the cropped volu…

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## [Export Mask as binary tiff file ](https://discourse.slicer.org/t/export-mask-as-binary-tiff-file/2329)

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**Author:** [@LisaWies](https://discourse.slicer.org/u/LisaWies)\
**Replies:** 2\
**Last updated:** [April 19, 2018, 7:01am UTC](https://discourse.slicer.org/t/export-mask-as-binary-tiff-file/2329 "2018-04-19T07:01:16Z")

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Hi everyone, I’m trying to export my generated mask as a set of binary files for each slice. How can I achieve this in Slicer? Thanks a lot for your help. Best wishes, Lisa

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## [How to compare two bone?](https://discourse.slicer.org/t/how-to-compare-two-bone/2628)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 0\
**Last updated:** [April 19, 2018, 5:26am UTC](https://discourse.slicer.org/t/how-to-compare-two-bone/2628 "2018-04-19T05:26:50Z")

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How to compare two bone with a color map. The method was discribled as follows: The thickness was calculated using Scanco’s trabecular bone evaluation (Direct method). Color maps of the thickness were generated from…

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## [can't find batch processing](https://discourse.slicer.org/t/cant-find-batch-processing/2620)

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**Author:** [@roostIR](https://discourse.slicer.org/u/roostIR)\
**Replies:** 1\
**Last updated:** [April 18, 2018, 3:58pm UTC](https://discourse.slicer.org/t/cant-find-batch-processing/2620 "2018-04-18T15:58:39Z")

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Operating system: MACOSX high sierra Slicer version: 4.8.1 Expected behavior: to click on modules and see batch processing option Actual behavior: there is no batch processing option under module list Hi everyone - t…

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## [fixing the distorted shape of segmented organs](https://discourse.slicer.org/t/fixing-the-distorted-shape-of-segmented-organs/2625)

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**Author:** [@mmansouri](https://discourse.slicer.org/u/mmansouri)\
**Replies:** 1\
**Last updated:** [April 18, 2018, 2:24pm UTC](https://discourse.slicer.org/t/fixing-the-distorted-shape-of-segmented-organs/2625 "2018-04-18T14:24:29Z")

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we need to segment all the body organs using a pediatric whole body MRI. I know that my MRI quality is highly anisotropic (0.781250, 0.781250, 3.900000). When I use the segmentation tool, the quality of outcome 3D mod…

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## [Problem with saving](https://discourse.slicer.org/t/problem-with-saving/2611)

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**Author:** [@rakusb](https://discourse.slicer.org/u/rakusb)\
**Replies:** 11\
**Last updated:** [April 18, 2018, 1:04pm UTC](https://discourse.slicer.org/t/problem-with-saving/2611 "2018-04-18T13:04:55Z")

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Hi, I have problem with saving anything in Slicer 4.8.0. What i do wrong? Here you have screen

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## [DICOM of femur or hip joint for project](https://discourse.slicer.org/t/dicom-of-femur-or-hip-joint-for-project/2616)

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**Author:** [@ewa](https://discourse.slicer.org/u/ewa)\
**Replies:** 1\
**Last updated:** [April 17, 2018, 9:21pm UTC](https://discourse.slicer.org/t/dicom-of-femur-or-hip-joint-for-project/2616 "2018-04-17T21:21:03Z")

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Hello every one ! Do you maybe any CT or MRI DICOMs of femur or all hip joint? I have a project for my studies and I have to create a hip endoprothesis. I would be very thankful.

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