# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=303

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

**Page:** 304

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## [Portable installation of Slicer with extension on USB](https://discourse.slicer.org/t/portable-installation-of-slicer-with-extension-on-usb/8582)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 8\
**Last updated:** [January 8, 2021, 7:16pm UTC](https://discourse.slicer.org/t/portable-installation-of-slicer-with-extension-on-usb/8582 "2021-01-08T19:16:09Z")

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I need a Slicer installation on a USB stick with SlicerMorph and other extensions installed for portability reasons. While I can install Slicer on the USB stick and the extensions to a folder within the USB stick, those…

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## [Changing folder colors, changes the normals of segmentation 3D surface inside of that folder](https://discourse.slicer.org/t/changing-folder-colors-changes-the-normals-of-segmentation-3d-surface-inside-of-that-folder/15396)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 3\
**Last updated:** [January 8, 2021, 4:46pm UTC](https://discourse.slicer.org/t/changing-folder-colors-changes-the-normals-of-segmentation-3d-surface-inside-of-that-folder/15396 "2021-01-08T16:46:59Z")

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This only happens to one segmentation I am working on… Other segmentations look perfectly fine. I realized that I can put hundreds of segmentations into one folder and change the color for the entire folder and that…

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## [Coordinate system](https://discourse.slicer.org/t/coordinate-system/15404)

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**Author:** [@danila](https://discourse.slicer.org/u/danila)\
**Replies:** 1\
**Last updated:** [January 8, 2021, 4:17pm UTC](https://discourse.slicer.org/t/coordinate-system/15404 "2021-01-08T16:17:12Z")

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Hi, I have an STL file of a virtual surgical planning and I would like to compare it with the 3D model, obtained from a post-operative CBCT. The goal is to evaluate the accuracy of the VSP. When I load the two files (S…

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## [Segmentation Editor - painting also selects in previous and next image](https://discourse.slicer.org/t/segmentation-editor-painting-also-selects-in-previous-and-next-image/15408)

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**Author:** [@willi](https://discourse.slicer.org/u/willi)\
**Replies:** 2\
**Last updated:** [January 8, 2021, 3:40pm UTC](https://discourse.slicer.org/t/segmentation-editor-painting-also-selects-in-previous-and-next-image/15408 "2021-01-08T15:40:32Z")

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Hello, I am fairly new to 3D Slicer. It looks really good to me and I want to use it for my research. I did some segmentation with data I had from previous studies and everything worked pretty good and as expected! Un…

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## [Step effect on the exported STL models](https://discourse.slicer.org/t/step-effect-on-the-exported-stl-models/15392)

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**Author:** [@Tekk\_ya](https://discourse.slicer.org/u/Tekk_ya)\
**Replies:** 8\
**Last updated:** [January 8, 2021, 3:31pm UTC](https://discourse.slicer.org/t/step-effect-on-the-exported-stl-models/15392 "2021-01-08T15:31:59Z")

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Hi, I have segmented the desired organs in a CT scan, and after applying a different type of smoothing such as median smoothing and joint smoothing I export the models as STL files. However, I see some “step effect” on …

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## [Calculating the deformation](https://discourse.slicer.org/t/calculating-the-deformation/15371)

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**Author:** [@BORIPHAT](https://discourse.slicer.org/u/BORIPHAT)\
**Replies:** 4\
**Last updated:** [January 8, 2021, 5:14am UTC](https://discourse.slicer.org/t/calculating-the-deformation/15371 "2021-01-08T05:14:06Z")

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Hello, I have the two CT image data sets of breast phantom (the same body size but different breast size). I would like to know how much it deformed? Firstly, I use the segmentation comparison module to get HD and DICE…

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## [When transfering segment from 1 segmentation to another resolution changes](https://discourse.slicer.org/t/when-transfering-segment-from-1-segmentation-to-another-resolution-changes/15370)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 7\
**Last updated:** [January 7, 2021, 8:40pm UTC](https://discourse.slicer.org/t/when-transfering-segment-from-1-segmentation-to-another-resolution-changes/15370 "2021-01-07T20:40:42Z")

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So I just move the segment from one segmentation (cropped volume long time ago ) to this new segmentation (not cropped but full volume little bit modified position) This is what I end up with… I wonder why?! The im…

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## [Determine if a transform node contains actual transformation or is identity](https://discourse.slicer.org/t/determine-if-a-transform-node-contains-actual-transformation-or-is-identity/15387)

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**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 3\
**Last updated:** [January 7, 2021, 4:53pm UTC](https://discourse.slicer.org/t/determine-if-a-transform-node-contains-actual-transformation-or-is-identity/15387 "2021-01-07T16:53:22Z")

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I wonder if there is a simple way to determine if a transform node is identity or not. The reason why it is not trivial is that such a node can contain a linear transform in which case it is simple, but can also contain …

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## [SegmentEditor error](https://discourse.slicer.org/t/segmenteditor-error/15355)

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**Author:** [@mohsenp](https://discourse.slicer.org/u/mohsenp)\
**Replies:** 8\
**Last updated:** [January 7, 2021, 2:05pm UTC](https://discourse.slicer.org/t/segmenteditor-error/15355 "2021-01-07T14:05:19Z")

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Operating system: Slicer version:Slicer 4.11.20200930 Expected behavior: Actual behavior: hi , I have a problem with segment editor module in 3d slicer . Warning, the module “SegmentEditor” has no widget representa…

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## [Importing several single DICOM files as a merged and stacked DICOM file](https://discourse.slicer.org/t/importing-several-single-dicom-files-as-a-merged-and-stacked-dicom-file/15381)

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**Author:** [@Ata\_Naghavi](https://discourse.slicer.org/u/Ata_Naghavi)\
**Replies:** 1\
**Last updated:** [January 7, 2021, 1:23am UTC](https://discourse.slicer.org/t/importing-several-single-dicom-files-as-a-merged-and-stacked-dicom-file/15381 "2021-01-07T01:23:51Z")

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Operating system: Windows 10 Slicer version: 4.13.0 Expected behavior: To be able to view and segment my imported DICOM files as a merged file and can go through them slice by slice. Actual behavior: After importing m…

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## [Elastix registration problem](https://discourse.slicer.org/t/elastix-registration-problem/15347)

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**Author:** [@opetne](https://discourse.slicer.org/u/opetne)\
**Replies:** 1\
**Last updated:** [January 7, 2021, 1:21am UTC](https://discourse.slicer.org/t/elastix-registration-problem/15347 "2021-01-07T01:21:56Z")

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Operating system: Windows10 Slicer version:4.11.20200930 Expected behavior:Registration 2 MR volumes Actual behavior: Volume registration is started in working directory: C:/Users/petnehazyors/AppData/Local/Temp/Slic…

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## [Error in exporting .tiff images to DICOM](https://discourse.slicer.org/t/error-in-exporting-tiff-images-to-dicom/15378)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 3\
**Last updated:** [January 7, 2021, 12:29am UTC](https://discourse.slicer.org/t/error-in-exporting-tiff-images-to-dicom/15378 "2021-01-07T00:29:21Z")

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Hello, I have .tiff files of a lung phantom that I want to export to DICOM files using 3D Slicer (4.11.20200930 or 4.13.0). I was able to import the .tiff files into 3D Slicer and export them to DICOM. But when I tried …

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## [Export images with markups](https://discourse.slicer.org/t/export-images-with-markups/15377)

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**Author:** [@zulex](https://discourse.slicer.org/u/zulex)\
**Replies:** 1\
**Last updated:** [January 6, 2021, 3:38pm UTC](https://discourse.slicer.org/t/export-images-with-markups/15377 "2021-01-06T15:38:59Z")

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@lassoan, I’m currently using screen capture to export the image sequence as png with markup visualized. The only problem I’m finding is that it exactly captures the dimensions of the screen instead of the volume (I kno…

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## [How to fix "Error occured during ITK connversion" Error](https://discourse.slicer.org/t/how-to-fix-error-occured-during-itk-connversion-error/14381)

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**Author:** [@gipson04](https://discourse.slicer.org/u/gipson04)\
**Replies:** 6\
**Last updated:** [January 6, 2021, 3:34pm UTC](https://discourse.slicer.org/t/how-to-fix-error-occured-during-itk-connversion-error/14381 "2021-01-06T15:34:49Z")

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Hi I tend to compare contours from 2 Rt structure files from pinnacle using Segment comparison tool. When i loaded the the files and computed similarity matrix i got a error stating ‘Error occurred during ITK connversio…

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## [Ultrasound and CT image fusion](https://discourse.slicer.org/t/ultrasound-and-ct-image-fusion/15077)

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**Author:** [@Nsangu](https://discourse.slicer.org/u/Nsangu)\
**Replies:** 16\
**Last updated:** [January 6, 2021, 1:56pm UTC](https://discourse.slicer.org/t/ultrasound-and-ct-image-fusion/15077 "2021-01-06T13:56:45Z")

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Greetings. My name is Augustine, A medical Physicist from Zambia. Iam working on trying to fuse US images with CT and I have a lot of questions. My area of interest is the pelvic region (the cervix) in particular. I ha…

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## [Harden transformation in batches](https://discourse.slicer.org/t/harden-transformation-in-batches/15367)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 2\
**Last updated:** [January 6, 2021, 5:36am UTC](https://discourse.slicer.org/t/harden-transformation-in-batches/15367 "2021-01-06T05:36:46Z")

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How do I harden transformation for 100 segmentations… Normally I have to right click them all and click harden transformation for each segmentation. Is there any way to do it at once?

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## [Taking one segmentation and inserting it into another but other one has very small volume](https://discourse.slicer.org/t/taking-one-segmentation-and-inserting-it-into-another-but-other-one-has-very-small-volume/15368)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 3\
**Last updated:** [January 6, 2021, 4:28am UTC](https://discourse.slicer.org/t/taking-one-segmentation-and-inserting-it-into-another-but-other-one-has-very-small-volume/15368 "2021-01-06T04:28:02Z")

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So when I didn’t have much ram, I was cropping volume and then working with small volume segmenting only what needed there. Then I cropped another part of that big main volume and segmented another thing. Then I pulled…

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## [Creating a lumen from an STL file](https://discourse.slicer.org/t/creating-a-lumen-from-an-stl-file/15204)

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**Author:** [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Replies:** 2\
**Last updated:** [January 6, 2021, 1:15am UTC](https://discourse.slicer.org/t/creating-a-lumen-from-an-stl-file/15204 "2021-01-06T01:15:45Z")

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Hello everyone, I attached cylinders to my vessel model using CAD software and saved them as STL file and printed them. I poured epoxy resin into the printed vessel model to recreate the lumen. Unfortunately, I did not …

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## [Unable to load a segmentation encoded as .tag file](https://discourse.slicer.org/t/unable-to-load-a-segmentation-encoded-as-tag-file/15271)

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**Author:** [@Maxnach](https://discourse.slicer.org/u/Maxnach)\
**Replies:** 11\
**Last updated:** [January 5, 2021, 8:30pm UTC](https://discourse.slicer.org/t/unable-to-load-a-segmentation-encoded-as-tag-file/15271 "2021-01-05T20:30:08Z")

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Operating system: Windows 10 Slicer version: 4.13.0 Expected behavior: Load pre-existing segmentation .tag file Actual behavior: Unable to load Hello 3Dslicer community, I’m just starting with this amazing software.…

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## [Need to get numeric data from comparing two different segmentations](https://discourse.slicer.org/t/need-to-get-numeric-data-from-comparing-two-different-segmentations/15358)

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**Author:** [@Maria\_Alvarez\_Flores](https://discourse.slicer.org/u/Maria_Alvarez_Flores)\
**Replies:** 0\
**Last updated:** [January 5, 2021, 8:29pm UTC](https://discourse.slicer.org/t/need-to-get-numeric-data-from-comparing-two-different-segmentations/15358 "2021-01-05T20:29:03Z")

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Operating system: Windows 10 Slicer version:4.11 Hi there! I´m trying to compare different segmentations and evaluate them with numeric results. The aim is to compare growcut segmentation with otsu threshold and with …

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## [3D model load in as segmentation, how?](https://discourse.slicer.org/t/3d-model-load-in-as-segmentation-how/15351)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 1\
**Last updated:** [January 5, 2021, 6:58pm UTC](https://discourse.slicer.org/t/3d-model-load-in-as-segmentation-how/15351 "2021-01-05T18:58:32Z")

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How can a 3d obj file be loaded in and converted to seg.nrrd?

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## [Number of voxels dependent on HU value](https://discourse.slicer.org/t/number-of-voxels-dependent-on-hu-value/15317)

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**Author:** [@seymakandemir](https://discourse.slicer.org/u/seymakandemir)\
**Replies:** 4\
**Last updated:** [January 5, 2021, 10:33am UTC](https://discourse.slicer.org/t/number-of-voxels-dependent-on-hu-value/15317 "2021-01-05T10:33:00Z")

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Hi all, I created a segment of volume and got the histogram of segment. What I need to do next is to have statistical data about segment such as; How many voxels above/under 2000 HU value? And their percentage? I could…

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## [Applying color to the entire folder, turns the surfaces inside out! flips verticals in 3d models why?](https://discourse.slicer.org/t/applying-color-to-the-entire-folder-turns-the-surfaces-inside-out-flips-verticals-in-3d-models-why/15344)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 0\
**Last updated:** [January 5, 2021, 3:32am UTC](https://discourse.slicer.org/t/applying-color-to-the-entire-folder-turns-the-surfaces-inside-out-flips-verticals-in-3d-models-why/15344 "2021-01-05T03:32:32Z")

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Applying color to the entire folder which contains multiple segmentations and segments in these segmentations, turns the surfaces inside out! flips verticals in 3d models why? in error log only this shows many times: G…

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## [Segmentation using Thresholding in MRI Scan](https://discourse.slicer.org/t/segmentation-using-thresholding-in-mri-scan/15343)

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**Author:** [@JacobD](https://discourse.slicer.org/u/JacobD)\
**Replies:** 1\
**Last updated:** [January 4, 2021, 11:47pm UTC](https://discourse.slicer.org/t/segmentation-using-thresholding-in-mri-scan/15343 "2021-01-04T23:47:44Z")

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Hello, I am attempting to segment bone from a shoulder MRI. Using the threshold feature, I have been able to select the humerus and scapula so that they can be modeled, however, there is other area highlighted that matc…

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## [Where can I download DICOMs?](https://discourse.slicer.org/t/where-can-i-download-dicoms/15323)

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**Author:** [@sergiGB](https://discourse.slicer.org/u/sergiGB)\
**Replies:** 4\
**Last updated:** [January 4, 2021, 5:39pm UTC](https://discourse.slicer.org/t/where-can-i-download-dicoms/15323 "2021-01-04T17:39:56Z")

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I need DICOMS for a work but I dont know where can I get them, thanks so much

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## [Apply Filter to Multivolume](https://discourse.slicer.org/t/apply-filter-to-multivolume/15336)

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**Author:** [@nlampen](https://discourse.slicer.org/u/nlampen)\
**Replies:** 0\
**Last updated:** [January 4, 2021, 4:41pm UTC](https://discourse.slicer.org/t/apply-filter-to-multivolume/15336 "2021-01-04T16:41:15Z")

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Hello all! I’m relatively new to 3D Slicer. I am currently using the T2 mapping module on knee scans, but I am wondering if I can apply a filter (specifically the gradient anisotropic diffusion image filter from ITK) to …

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## [Slice display - why image in slicer is more smoothing](https://discourse.slicer.org/t/slice-display-why-image-in-slicer-is-more-smoothing/15259)

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**Author:** [@czj1989](https://discourse.slicer.org/u/czj1989)\
**Replies:** 4\
**Last updated:** [January 4, 2021, 1:11am UTC](https://discourse.slicer.org/t/slice-display-why-image-in-slicer-is-more-smoothing/15259 "2021-01-04T01:11:05Z")

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Hello! It is not a bug. I just wonder something about the slice display in Slicer. when I used vtk6.2 to display image with vtkImageReslice::SetInterpolationModeToLinear() and vtkImageActor:InterpolateOn(), I got Figure …

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## [Error with calculation image difference using ROI](https://discourse.slicer.org/t/error-with-calculation-image-difference-using-roi/15315)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 3\
**Last updated:** [January 3, 2021, 7:32pm UTC](https://discourse.slicer.org/t/error-with-calculation-image-difference-using-roi/15315 "2021-01-03T19:32:34Z")

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Slicer version: 4.13.0 and Slicer 4.11.20200930 Hello everyone, I want to calculate the image difference between the fixed and warped image, after registration, using a specified ROI. I manually created the ROI, but af…

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## [Failed to execute in CentOS 8.3.2011](https://discourse.slicer.org/t/failed-to-execute-in-centos-8-3-2011/15310)

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**Author:** [@endi](https://discourse.slicer.org/u/endi)\
**Replies:** 4\
**Last updated:** [January 2, 2021, 12:49am UTC](https://discourse.slicer.org/t/failed-to-execute-in-centos-8-3-2011/15310 "2021-01-02T00:49:59Z")

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I downloaded the latest stable release and was not able to get Slicer to execute. The error message received was /u/software/slicer/Slicer-4.11.20200930-linux-amd64/bin/SlicerApp-real: error while loading shared librari…

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## [Influence of spacing on quality](https://discourse.slicer.org/t/influence-of-spacing-on-quality/14999)

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**Author:** [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Replies:** 35\
**Last updated:** [January 1, 2021, 9:49pm UTC](https://discourse.slicer.org/t/influence-of-spacing-on-quality/14999 "2021-01-01T21:49:01Z")

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Hello everyone, I’m trying to reduce the spacing using cropped volume in order to create very thin walls with a uniform thickness, but the spacing of the cropped volume is again at 0.2826 mm. So it makes no difference w…

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