# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=165

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

**Page:** 166

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## [Strange Issues with volumes and segments](https://discourse.slicer.org/t/strange-issues-with-volumes-and-segments/29201)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 1\
**Last updated:** [April 29, 2023, 12:49pm UTC](https://discourse.slicer.org/t/strange-issues-with-volumes-and-segments/29201 "2023-04-29T12:49:30Z")

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Slicer 5.2.2 (5.3 same) windows desktop w GPU Loading clinical CT dataset va DICOM mechanism into slicer Saving the volume as nrdd and in a mrb file (129 MB) Do a lung segmentation and an emphysema analysis After the…

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## [Saving DICOMsegmentations - Interoperability with OHIF](https://discourse.slicer.org/t/saving-dicomsegmentations-interoperability-with-ohif/29037)

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**Author:** [@ksidis](https://discourse.slicer.org/u/ksidis)\
**Replies:** 10\
**Last updated:** [April 28, 2023, 8:24pm UTC](https://discourse.slicer.org/t/saving-dicomsegmentations-interoperability-with-ohif/29037 "2023-04-28T20:24:34Z")

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I am using 3Dslicer with the Monailabel plugin to run some segmentation models. The result is then exported as DICOMSegmentation and saved to an Orthanc PACS. Up to this point we were using OHIF v2 to visualise the image…

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## [Set view perpendicular to a Markup Line](https://discourse.slicer.org/t/set-view-perpendicular-to-a-markup-line/29153)

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**Author:** [@mahi2208](https://discourse.slicer.org/u/mahi2208)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 6:19pm UTC](https://discourse.slicer.org/t/set-view-perpendicular-to-a-markup-line/29153 "2023-04-28T18:19:56Z")

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Hi, I am relatively new to Slicer and not sure how to do thiis. Here is some background for what I am trying to do: I draw a line using markupsLine to depict a possible path for a neurosurgical procedure. I need to be…

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## [I need to generate a histogram of intensities! ](https://discourse.slicer.org/t/i-need-to-generate-a-histogram-of-intensities/19621)

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**Author:** [@debadrita\_jana](https://discourse.slicer.org/u/debadrita_jana)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 4:12pm UTC](https://discourse.slicer.org/t/i-need-to-generate-a-histogram-of-intensities/19621 "2023-04-28T16:12:13Z")

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Operating system:Windows Slicer version:4.11.20210226 Expected behavior: Copy pasting the code is not working Actual behavior: Errors are showing up

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## [Lung lobe segmentation using 3D slicer](https://discourse.slicer.org/t/lung-lobe-segmentation-using-3d-slicer/29060)

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**Author:** [@Rajesh\_Ds](https://discourse.slicer.org/u/Rajesh_Ds)\
**Replies:** 3\
**Last updated:** [April 28, 2023, 11:10am UTC](https://discourse.slicer.org/t/lung-lobe-segmentation-using-3d-slicer/29060 "2023-04-28T11:10:57Z")

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How can I get lung lobe segmentation (into RUL, RML, RLL, LUL and LLL) given a CT volume ? Which is the best method in slicer ? Please let me know. I want something like this: I have tried interactive lobe segmentat…

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## [SRep module is not loading from SkeletalRepresentation extension](https://discourse.slicer.org/t/srep-module-is-not-loading-from-skeletalrepresentation-extension/28977)

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**Author:** [@DRDMT](https://discourse.slicer.org/u/DRDMT)\
**Replies:** 4\
**Last updated:** [April 28, 2023, 8:59am UTC](https://discourse.slicer.org/t/srep-module-is-not-loading-from-skeletalrepresentation-extension/28977 "2023-04-28T08:59:57Z")

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Hello Team, I installed the “SkeletalRepresentation” Extension from " @KitwareMedical/slicer-extensions-webapp" I used the Slicer Extension Manager feature to do the same. But the module is not loading. Kindly see at…

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## [SegmentStatistics error in Python](https://discourse.slicer.org/t/segmentstatistics-error-in-python/29171)

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**Author:** [@Markb](https://discourse.slicer.org/u/Markb)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 7:58am UTC](https://discourse.slicer.org/t/segmentstatistics-error-in-python/29171 "2023-04-28T07:58:45Z")

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Hi. I have a bunch of segments in an RTStruct file, and a bunch of images that I want to get some statistics from. Doing this manually is a bit of a timehog, so I looked into writing a quick python script and running it …

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## [Reads DCM volume with grid transform with python](https://discourse.slicer.org/t/reads-dcm-volume-with-grid-transform-with-python/28998)

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**Author:** [@Thirawat](https://discourse.slicer.org/u/Thirawat)\
**Replies:** 4\
**Last updated:** [April 28, 2023, 4:33am UTC](https://discourse.slicer.org/t/reads-dcm-volume-with-grid-transform-with-python/28998 "2023-04-28T04:33:40Z")

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Hi all, I want to read a DCM file and output it with the transform contained in the file. But now that I’m using SimpleITK, it only outputs untransformed DCM files. Can you suggest a method? My code: def readDCM(fol…

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## [Transforme segmentaion](https://discourse.slicer.org/t/transforme-segmentaion/29150)

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**Author:** [@Thirawat](https://discourse.slicer.org/u/Thirawat)\
**Replies:** 4\
**Last updated:** [April 28, 2023, 4:31am UTC](https://discourse.slicer.org/t/transforme-segmentaion/29150 "2023-04-28T04:31:46Z")

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I annotated a big dataset (for me), but the Dicom file of the CT scan has transformed (I get this from start). when I use this segment in Python by simpleITK \[The problem post\] it will not match with the CT image beca…

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## [Shift scale image filter](https://discourse.slicer.org/t/shift-scale-image-filter/29178)

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**Author:** [@mahmood](https://discourse.slicer.org/u/mahmood)\
**Replies:** 0\
**Last updated:** [April 27, 2023, 8:05pm UTC](https://discourse.slicer.org/t/shift-scale-image-filter/29178 "2023-04-27T20:05:32Z")

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Sorry, I have a question? What’s the shift scale image filter in 3dslicer? Is that (mu +/- 3sigma)? If yes, what numbers should be put in shift and scale values to make the above formula? And what’s shift and scale i…

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## [Radiomics features from more CT studies](https://discourse.slicer.org/t/radiomics-features-from-more-ct-studies/29176)

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**Author:** [@Tomas\_Korinek](https://discourse.slicer.org/u/Tomas_Korinek)\
**Replies:** 1\
**Last updated:** [April 27, 2023, 5:43pm UTC](https://discourse.slicer.org/t/radiomics-features-from-more-ct-studies/29176 "2023-04-27T17:43:19Z")

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Please, is there any way extract radiomics features from Slicer 3D application in “one step”? I mean. I have 200 patient studies (CTs, RT Structure Sets). I can load them in Slicer 3D. I would like to extract radiomic…

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## [How to export color node as color table](https://discourse.slicer.org/t/how-to-export-color-node-as-color-table/29134)

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**Author:** [@dyollb](https://discourse.slicer.org/u/dyollb)\
**Replies:** 1\
**Last updated:** [April 27, 2023, 2:31pm UTC](https://discourse.slicer.org/t/how-to-export-color-node-as-color-table/29134 "2023-04-27T14:31:27Z")

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I would like to convert a slicer .seg.nrrd segmentation into a labelmap + color table, so I can use it downstream in other applications. I figured out how to convert the segmentation to a labelmap and I can see the color…

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## [Extension download issues in govcloud](https://discourse.slicer.org/t/extension-download-issues-in-govcloud/29173)

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**Author:** [@bbkonk](https://discourse.slicer.org/u/bbkonk)\
**Replies:** 1\
**Last updated:** [April 27, 2023, 1:40pm UTC](https://discourse.slicer.org/t/extension-download-issues-in-govcloud/29173 "2023-04-27T13:40:44Z")

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I have slicer installed on a Windows ec2 instance in govcloud. I’ve tried a few versions (5.2.1, 5.2.2, 5.3.0). If I attempt to install from extensions manager, I receive “Failed downloading: https://slicer-packages.kit…

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## [ImageStream-Cropping Plus/3dSlicer](https://discourse.slicer.org/t/imagestream-cropping-plus-3dslicer/29162)

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**Author:** [@alex\_johnson](https://discourse.slicer.org/u/alex_johnson)\
**Replies:** 0\
**Last updated:** [April 27, 2023, 2:34am UTC](https://discourse.slicer.org/t/imagestream-cropping-plus-3dslicer/29162 "2023-04-27T02:34:34Z")

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Hello, I have encountered a problem while trying to Crop a transmitted image stream from a Video Capture Card to Slicer. The stream is working fine but in 3dSlicer the images stay unchanged. I’ve already tried the ClipR…

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## [having vmtk installed but not found in the toolbar](https://discourse.slicer.org/t/having-vmtk-installed-but-not-found-in-the-toolbar/29154)

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**Author:** [@Yvonne](https://discourse.slicer.org/u/Yvonne)\
**Replies:** 2\
**Last updated:** [April 27, 2023, 8:26am UTC](https://discourse.slicer.org/t/having-vmtk-installed-but-not-found-in-the-toolbar/29154 "2023-04-27T08:26:27Z")

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Hi, I’m using a Win 10 system with Python 3.11 and Anaconda 2022 installed. I’ve installed the toolkit via the ‘extensions manager’ (please see the attached) however still couldn’t find it on the toolbar. (From Slicer …

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## [Show only selected 'jump slice' control point , hide other other control points](https://discourse.slicer.org/t/show-only-selected-jump-slice-control-point-hide-other-other-control-points/29160)

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**Author:** [@Kae1](https://discourse.slicer.org/u/Kae1)\
**Replies:** 0\
**Last updated:** [April 27, 2023, 12:00am UTC](https://discourse.slicer.org/t/show-only-selected-jump-slice-control-point-hide-other-other-control-points/29160 "2023-04-27T00:00:28Z")

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I have a range of implanted stereo EEG electrode contacts in my mark up file and am using the ‘jump slice’ function in Markups/Control Points to view selected electrode/contacts in the three axis. However when I ‘jump sl…

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## [Loading multiple MRI series (T1, T2, FLAIR, ...) under one subject](https://discourse.slicer.org/t/loading-multiple-mri-series-t1-t2-flair-under-one-subject/29096)

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**Author:** [@laurentletg](https://discourse.slicer.org/u/laurentletg)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 10:13pm UTC](https://discourse.slicer.org/t/loading-multiple-mri-series-t1-t2-flair-under-one-subject/29096 "2023-04-26T22:13:12Z")

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Hello, I am currently working on the BraTS dataset with different MRI sequences (T1, T2, FLAIR, T1CE) saved as separate \*.nii.gz files. I am trying to write a script that can load all sequences under a subject so that t…

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## [How to visualize a 3D skeleton image](https://discourse.slicer.org/t/how-to-visualize-a-3d-skeleton-image/29155)

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**Author:** [@Peidi\_Xu](https://discourse.slicer.org/u/Peidi_Xu)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 9:39pm UTC](https://discourse.slicer.org/t/how-to-visualize-a-3d-skeleton-image/29155 "2023-04-26T21:39:16Z")

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I have a simple 3D binary in .nii.gz form, where voxel value 1 means foreground and 0 means background. So it is a skeleton because every foreground voxel has a thickness of one, e.g., it is the output after running skim…

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## [Segmenting in a rotated volume](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147)

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**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 2\
**Last updated:** [April 26, 2023, 8:27pm UTC](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147 "2023-04-26T20:27:22Z")

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Hello dear community, it is me again. I made the following observation which induced a question: Goal: to segment a rotated volume Observation: if I create a new segment first and then rotate the volume in the ‘Transfo…

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## [How to change placeholder text in ctkCheckableComboBox](https://discourse.slicer.org/t/how-to-change-placeholder-text-in-ctkcheckablecombobox/29144)

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**Author:** [@Mauricio\_Cespedes](https://discourse.slicer.org/u/Mauricio_Cespedes)\
**Replies:** 3\
**Last updated:** [April 26, 2023, 4:07pm UTC](https://discourse.slicer.org/t/how-to-change-placeholder-text-in-ctkcheckablecombobox/29144 "2023-04-26T16:07:11Z")

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Hi, I’m currently building an extension and I’m using a few ctkCheckableComboBox widgets, which I’m creating in a .ui file and then loading on my Python script for the extension I’m building. I’m wondering if there’s any…

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## [Patched DICOM will not open as Image Sequence](https://discourse.slicer.org/t/patched-dicom-will-not-open-as-image-sequence/28910)

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**Author:** [@Tannadrake](https://discourse.slicer.org/u/Tannadrake)\
**Replies:** 12\
**Last updated:** [April 26, 2023, 2:51pm UTC](https://discourse.slicer.org/t/patched-dicom-will-not-open-as-image-sequence/28910 "2023-04-26T14:51:23Z")

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I am attempting to open a DICOM image that required patching. I used the DICOM Patcher module, then when I attempt to open an imaging sequence it gives me an error saying it cannot open as an Image Sequence. This is the…

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## [NRRD Segmentation To Numpy problem](https://discourse.slicer.org/t/nrrd-segmentation-to-numpy-problem/29122)

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**Author:** [@Thirawat](https://discourse.slicer.org/u/Thirawat)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 9:55am UTC](https://discourse.slicer.org/t/nrrd-segmentation-to-numpy-problem/29122 "2023-04-26T09:55:18Z")

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Hi, All I have .nrrd files of segmentations, so I only have 2 classes. but not all each file have 2 classes, I can say that most of them are one class for one file. then let’s talk about my problem. I try to take seg…

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## [Increasing ALPACA Non-Rigid Alignment](https://discourse.slicer.org/t/increasing-alpaca-non-rigid-alignment/28906)

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**Author:** [@evaherbst](https://discourse.slicer.org/u/evaherbst)\
**Replies:** 13\
**Last updated:** [April 26, 2023, 8:47am UTC](https://discourse.slicer.org/t/increasing-alpaca-non-rigid-alignment/28906 "2023-04-26T08:47:45Z")

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Hello, I am currently testing ALPACA to transfer muscle attachment landmarks from one scapula to another for patient specific modeling. The rigid alignment seems to work pretty well, but the deformable alignment is not…

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## [Running python script in slicer in linux](https://discourse.slicer.org/t/running-python-script-in-slicer-in-linux/29124)

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**Author:** [@exngan](https://discourse.slicer.org/u/exngan)\
**Replies:** 3\
**Last updated:** [April 26, 2023, 8:33am UTC](https://discourse.slicer.org/t/running-python-script-in-slicer-in-linux/29124 "2023-04-26T08:33:40Z")

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Hi I tried to run python script or code in slicer in linux and windows (linux mainly). I followed this guideline, but none of the methods worked. I received syntax error everytime. https://slicer.readthedocs.io/en/lates…

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## [Programmatically (python) define the values for the min and max of the slider in the volume widget (not the min-max of the window/level)](https://discourse.slicer.org/t/programmatically-python-define-the-values-for-the-min-and-max-of-the-slider-in-the-volume-widget-not-the-min-max-of-the-window-level/28916)

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**Author:** [@RonJones](https://discourse.slicer.org/u/RonJones)\
**Replies:** 3\
**Last updated:** [April 26, 2023, 4:11am UTC](https://discourse.slicer.org/t/programmatically-python-define-the-values-for-the-min-and-max-of-the-slider-in-the-volume-widget-not-the-min-max-of-the-window-level/28916 "2023-04-26T04:11:41Z")

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I am trying to define the minimum and maximum values of the slides in the volume widget (see screenshot - it is the widgets circled in red). For clarity this is not the min-max of the WindowLevel. Which widget do th…

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## [Segmentation, using paint, the bulb of paint disappears after the image is oriented in accordance with the anatomical axes](https://discourse.slicer.org/t/segmentation-using-paint-the-bulb-of-paint-disappears-after-the-image-is-oriented-in-accordance-with-the-anatomical-axes/29128)

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**Author:** [@PolinaPostnikova](https://discourse.slicer.org/u/PolinaPostnikova)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 2:57am UTC](https://discourse.slicer.org/t/segmentation-using-paint-the-bulb-of-paint-disappears-after-the-image-is-oriented-in-accordance-with-the-anatomical-axes/29128 "2023-04-26T02:57:13Z")

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Hello colleagues! I am a new user of 3d slicer. I segment vertebrae, discs, dural sac on axial and sagittal MRI scans of the lumbar spine. After the image is oriented in accordance with the anatomical axes, the ability …

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## [Multi-volume rendering bug](https://discourse.slicer.org/t/multi-volume-rendering-bug/13939)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 8\
**Last updated:** [April 26, 2023, 1:04am UTC](https://discourse.slicer.org/t/multi-volume-rendering-bug/13939 "2023-04-26T01:04:45Z")

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Shading in the multi-volume rendering worked for a while for me, but in this dataset I am getting this error: Loaded volume from file: C:/Users/amaga/Desktop/Cuke\_9.9um\_2k\_\_rec\_Cor0556 Segment\_1\_1.nrrd. Dimensions: 326x…

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## [Error message:\[Qt\] ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1](https://discourse.slicer.org/t/error-message-qt-ctksliderwidget-setsinglestep-0-is-out-of-bounds-0-100-1/29064)

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**Author:** [@Dexter777](https://discourse.slicer.org/u/Dexter777)\
**Replies:** 1\
**Last updated:** [April 25, 2023, 11:39pm UTC](https://discourse.slicer.org/t/error-message-qt-ctksliderwidget-setsinglestep-0-is-out-of-bounds-0-100-1/29064 "2023-04-25T23:39:21Z")

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Hi, when I’m drawing a closed curve on a surface mesh to cut out and create a new surface model, I am receiving the following message: \[Qt\] ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1 The code I’m usi…

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## [Annotation screenshot\_Scale Factor](https://discourse.slicer.org/t/annotation-screenshot-scale-factor/29091)

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**Author:** [@leif2051](https://discourse.slicer.org/u/leif2051)\
**Replies:** 3\
**Last updated:** [April 25, 2023, 10:57pm UTC](https://discourse.slicer.org/t/annotation-screenshot-scale-factor/29091 "2023-04-25T22:57:08Z")

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Hi, I meet a problem when increasing the Scale Factor on Annotation Screenshot. How could I get the correct high-resolution image?

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## [CoodinateSystem mismatch when applying transform to mesh](https://discourse.slicer.org/t/coodinatesystem-mismatch-when-applying-transform-to-mesh/29117)

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**Author:** [@suranga](https://discourse.slicer.org/u/suranga)\
**Replies:** 0\
**Last updated:** [April 25, 2023, 2:09pm UTC](https://discourse.slicer.org/t/coodinatesystem-mismatch-when-applying-transform-to-mesh/29117 "2023-04-25T14:09:04Z")

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Hi, I have a trasform file and I want to apply this transform to a volumetric mesh which is in vtk unstructured grid format. I first load the mesh in RAS format and then apply the transformation and save to the disk us…

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