# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=36

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

**Page:** 37

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## [Is my perfusion file incomplete or am I incorrectly importing it? (DSC -\> rCBV)](https://discourse.slicer.org/t/is-my-perfusion-file-incomplete-or-am-i-incorrectly-importing-it-dsc-rcbv/43399)

<div class="topic-metadata">

**Author:** [@SegmenterSam](https://discourse.slicer.org/u/SegmenterSam)\
**Replies:** 4\
**Last updated:** [June 20, 2025, 3:44pm UTC](https://discourse.slicer.org/t/is-my-perfusion-file-incomplete-or-am-i-incorrectly-importing-it-dsc-rcbv/43399 "2025-06-20T15:44:21Z")

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Hello, I have a patient with a perfusion MRI which counts 925 slides originally in their electronic file. When exporting this file, our exporting software creates a folder with 37 files (925/25) and loading it into 3DSl…

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## [Oculomotor muscles segmentation in Total Segmentator](https://discourse.slicer.org/t/oculomotor-muscles-segmentation-in-total-segmentator/42585)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 6\
**Last updated:** [June 20, 2025, 7:03am UTC](https://discourse.slicer.org/t/oculomotor-muscles-segmentation-in-total-segmentator/42585 "2025-06-20T07:03:10Z")

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Hi, Jakob; Congratulations on the Oculomotor muscles segmentation you implemented in Total segmentator. I spent much time doing the 20 manual segmentations, but it was worth it. I tried your new module, and the results a…

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## [Crashing with some data](https://discourse.slicer.org/t/crashing-with-some-data/42166)

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**Author:** [@ValerieS](https://discourse.slicer.org/u/ValerieS)\
**Replies:** 13\
**Last updated:** [June 19, 2025, 11:44pm UTC](https://discourse.slicer.org/t/crashing-with-some-data/42166 "2025-06-19T23:44:19Z")

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Hi. I am working on Windows 11 and experiencing regular crashes with 3D Slicer. It is happing with data I have used in the past with no problem. I switched to my Mac lap top, same 3D slicer version (5.8.1), same data and…

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## [Opening ALPACA for the first time and stuck on "Installing ALPACA Python Packages...."](https://discourse.slicer.org/t/opening-alpaca-for-the-first-time-and-stuck-on-installing-alpaca-python-packages/43415)

<div class="topic-metadata">

**Author:** [@jsguerra](https://discourse.slicer.org/u/jsguerra)\
**Replies:** 3\
**Last updated:** [June 19, 2025, 4:37pm UTC](https://discourse.slicer.org/t/opening-alpaca-for-the-first-time-and-stuck-on-installing-alpaca-python-packages/43415 "2025-06-19T16:37:40Z")

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I recently upgraded my SSD and re-installed Slicermorph and the ALPACA extension. I went ahead and tried to open ALPACA for the first time since the new install and I seem to be stuck in the “Installing ALPACA Python Pac…

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## [Request to add the function of importing PerkinElmer's .vox format data](https://discourse.slicer.org/t/request-to-add-the-function-of-importing-perkinelmers-vox-format-data/42625)

<div class="topic-metadata">

**Author:** [@ggg](https://discourse.slicer.org/u/ggg)\
**Replies:** 8\
**Last updated:** [June 19, 2025, 2:44pm UTC](https://discourse.slicer.org/t/request-to-add-the-function-of-importing-perkinelmers-vox-format-data/42625 "2025-06-19T14:44:04Z")

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Hello everyone, my English level is not high, so many contents are translated by software, please forgive me if there are mistakes. I am currently using Bruker’s CTAn software to analyze data. Since I need to contact an…

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## [Build Error: Custom Module Appears in App but Build Exits with Code 1 (Slicer.rule and .rule Files)](https://discourse.slicer.org/t/build-error-custom-module-appears-in-app-but-build-exits-with-code-1-slicer-rule-and-rule-files/43420)

<div class="topic-metadata">

**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 0\
**Last updated:** [June 19, 2025, 1:50pm UTC](https://discourse.slicer.org/t/build-error-custom-module-appears-in-app-but-build-exits-with-code-1-slicer-rule-and-rule-files/43420 "2025-06-19T13:50:06Z")

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After integrating the custom modules into my Slicer-based application, I’m now getting the following error during the build process: Custom build for ‘E:\\Safe\\build\\CMakeFiles\\467e983c5e5c61d75f97be2c5e12c91e\\Slicer-mkd…

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## [Convert point cloud to surface model](https://discourse.slicer.org/t/convert-point-cloud-to-surface-model/21175)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 2\
**Last updated:** [June 19, 2025, 1:51pm UTC](https://discourse.slicer.org/t/convert-point-cloud-to-surface-model/21175 "2025-06-19T13:51:29Z")

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Hi andras, Is there a way to convert the point cloud (4colums, x,y,z,intensity) to surface model. Thank you Regards, Saima Safdar

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## [SetColor() in scripting lost all light reflection effect](https://discourse.slicer.org/t/setcolor-in-scripting-lost-all-light-reflection-effect/43398)

<div class="topic-metadata">

**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 5\
**Last updated:** [June 18, 2025, 9:20pm UTC](https://discourse.slicer.org/t/setcolor-in-scripting-lost-all-light-reflection-effect/43398 "2025-06-18T21:20:52Z")

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Whenever I set up color using modelNode.GetDisplayNode().SetColor() in Slicer Pytho console or a python script, the model appeared to lose all the light reflection and material effects. If I just click the color tabl…

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## [Creating a new extension module for real-time denoising integrating trained model (.h5 or .pth Model) into a custom module](https://discourse.slicer.org/t/creating-a-new-extension-module-for-real-time-denoising-integrating-trained-model-h5-or-pth-model-into-a-custom-module/43413)

<div class="topic-metadata">

**Author:** [@anpus](https://discourse.slicer.org/u/anpus)\
**Replies:** 0\
**Last updated:** [June 18, 2025, 6:09pm UTC](https://discourse.slicer.org/t/creating-a-new-extension-module-for-real-time-denoising-integrating-trained-model-h5-or-pth-model-into-a-custom-module/43413 "2025-06-18T18:09:51Z")

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I am currently working on integrating a “real-time denoising” into “3D Slicer (v 5.4.0)” by creating a “new extension module”. I have a trained “TensorFlow model saved in ‘.h5’ format” that I would like to deploy within …

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## [Higher resolution for screen captures of 3D view?](https://discourse.slicer.org/t/higher-resolution-for-screen-captures-of-3d-view/8880)

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**Author:** [@nick](https://discourse.slicer.org/u/nick)\
**Replies:** 54\
**Last updated:** [June 18, 2025, 2:49pm UTC](https://discourse.slicer.org/t/higher-resolution-for-screen-captures-of-3d-view/8880 "2025-06-18T14:49:49Z")

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Hello, I’m wondering if there’s a way to get higher resolution screen captures of the 3D view. I need images of my segmentations with a high enough dpi to print on a poster (about 300 is what I’m thinking). Is there a w…

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## [No length measurement in markups](https://discourse.slicer.org/t/no-length-measurement-in-markups/43404)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 2\
**Last updated:** [June 18, 2025, 10:51am UTC](https://discourse.slicer.org/t/no-length-measurement-in-markups/43404 "2025-06-18T10:51:10Z")

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Hi to everyone. Today working with the markups module I wanted to measure some segments, but when I create the markups, they do not show the length property (see picture). In curves, other properties like curvature and t…

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## [My segmentations disappear when trying to change the resolution](https://discourse.slicer.org/t/my-segmentations-disappear-when-trying-to-change-the-resolution/43394)

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**Author:** [@drew7](https://discourse.slicer.org/u/drew7)\
**Replies:** 3\
**Last updated:** [June 17, 2025, 8:44pm UTC](https://discourse.slicer.org/t/my-segmentations-disappear-when-trying-to-change-the-resolution/43394 "2025-06-17T20:44:38Z")

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Hi, I’m trying to change the resolution of a segmentation to then use a grow filter to adapt it to the vessel structures of my CTs. My problem is that, when setting any oversampling factor, my segmentation seemingly disa…

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## [nnUNET failed to load segmentation in DentalSegmentator & totalSegmentator](https://discourse.slicer.org/t/nnunet-failed-to-load-segmentation-in-dentalsegmentator-totalsegmentator/43374)

<div class="topic-metadata">

**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 6\
**Last updated:** [June 17, 2025, 6:41pm UTC](https://discourse.slicer.org/t/nnunet-failed-to-load-segmentation-in-dentalsegmentator-totalsegmentator/43374 "2025-06-17T18:41:00Z")

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I am using Ubuntu 22.04 and Slicer 5.9.0. The DentalSegmentator showed “failed to load segmentation; something is wrong with nnUnet processing” Here is the error log: \[DEBUG\]\[Qt\] 16.06.2025 15:08:12 \[\] (unknown:0) -…

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## [How to: DICOM stitching and exporting](https://discourse.slicer.org/t/how-to-dicom-stitching-and-exporting/43390)

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**Author:** [@Franchi](https://discourse.slicer.org/u/Franchi)\
**Replies:** 1\
**Last updated:** [June 17, 2025, 5:54pm UTC](https://discourse.slicer.org/t/how-to-dicom-stitching-and-exporting/43390 "2025-06-17T17:54:34Z")

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Hello everyone, total noob on 3DSlicer here! I have two partial cranial DICOM datasets of different length due to the unsufficient FOV of the CBCT used. It´s two different folders composed of 200 and 400 .dcm files eac…

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## [Description in markups lost when adding new markup](https://discourse.slicer.org/t/description-in-markups-lost-when-adding-new-markup/43392)

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**Author:** [@tvercaut](https://discourse.slicer.org/u/tvercaut)\
**Replies:** 4\
**Last updated:** [June 17, 2025, 5:16pm UTC](https://discourse.slicer.org/t/description-in-markups-lost-when-adding-new-markup/43392 "2025-06-17T17:16:54Z")

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Hi, I am interested in getting markup annotation in (MR) images. The markups would ideally be associated with descriptions. At the moment, unfortunately, it seems that any text added the description field is being lost …

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## [Error: \[VTK\] Input port 0 of algorithm vtkImageMapToWindowLevelColors (000001A807D0A830) has 0 connections but is not optional. \[VTK\] Input port 0 of algorithm vtkImageThreshold (000001A86BF0BB60) has 0 connections but is not optional.](https://discourse.slicer.org/t/error-vtk-input-port-0-of-algorithm-vtkimagemaptowindowlevelcolors-000001a807d0a830-has-0-connections-but-is-not-optional-vtk-input-port-0-of-algorithm-vtkimagethreshold-000001a86bf0bb60-has-0-connections-but-is-not-optional/43395)

<div class="topic-metadata">

**Author:** [@anpus](https://discourse.slicer.org/u/anpus)\
**Replies:** 2\
**Last updated:** [June 17, 2025, 5:08pm UTC](https://discourse.slicer.org/t/error-vtk-input-port-0-of-algorithm-vtkimagemaptowindowlevelcolors-000001a807d0a830-has-0-connections-but-is-not-optional-vtk-input-port-0-of-algorithm-vtkimagethreshold-000001a86bf0bb60-has-0-connections-but-is-not-optional/43395 "2025-06-17T17:08:00Z")

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Hi, I am using 3D slicer (Slicer version 5.4.0.) for improving the image quality in real-time by integrating .h5 model. But I’m getting a lot of errors in the console. \[VTK\] Input port 0 of algorithm vtkImageMapToWind…

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## [How to make the segmented trachea transparent](https://discourse.slicer.org/t/how-to-make-the-segmented-trachea-transparent/43396)

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**Author:** [@linyao](https://discourse.slicer.org/u/linyao)\
**Replies:** 2\
**Last updated:** [June 17, 2025, 5:05pm UTC](https://discourse.slicer.org/t/how-to-make-the-segmented-trachea-transparent/43396 "2025-06-17T17:05:07Z")

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Hello all. I am a radiologist and have found 3DSlicer to be incredibly useful. For my research I have the chest CT data where there is a foreign body with soft tissue intensity in the trachea. I hope to present the for…

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## [Segmenting a stomach after gastric sleeve](https://discourse.slicer.org/t/segmenting-a-stomach-after-gastric-sleeve/43391)

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**Author:** [@SanneGr](https://discourse.slicer.org/u/SanneGr)\
**Replies:** 0\
**Last updated:** [June 17, 2025, 4:36pm UTC](https://discourse.slicer.org/t/segmenting-a-stomach-after-gastric-sleeve/43391 "2025-06-17T16:36:46Z")

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Hi! I really like the TotalSegmentator extension in 3D Slicer. As of now, I’m trying to segment the stomach after gastric sleeve surgery. This surgery results in a smaller stomach with a different shape and this leads t…

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## [Issues with “open a dialog”](https://discourse.slicer.org/t/issues-with-open-a-dialog/43377)

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**Author:** [@doc-xie](https://discourse.slicer.org/u/doc-xie)\
**Replies:** 1\
**Last updated:** [June 17, 2025, 7:25am UTC](https://discourse.slicer.org/t/issues-with-open-a-dialog/43377 "2025-06-17T07:25:25Z")

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Hi everyone, In the “DICOM patcher” or “Diffusion-weighted DICOM Import (DICOM2niixGUI)” of Slicer(version-4.11.0), after click the button “open a dialog”, there is no any response or any dialog windows appeared. Moreov…

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## [SlicerMorph Photogrammetry photo masking issue](https://discourse.slicer.org/t/slicermorph-photogrammetry-photo-masking-issue/43369)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 14\
**Last updated:** [June 16, 2025, 11:47pm UTC](https://discourse.slicer.org/t/slicermorph-photogrammetry-photo-masking-issue/43369 "2025-06-16T23:47:30Z")

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I am trying the Slicer Photogrammetry with a student. The photos were taken by a cell phone at a single perspective. However, the masking behaved very weirdly. I’m also not very sure about the orientations. The pho…

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## [Slicer won't create a new database if the path contains a space](https://discourse.slicer.org/t/slicer-wont-create-a-new-database-if-the-path-contains-a-space/43320)

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**Author:** [@sconrad](https://discourse.slicer.org/u/sconrad)\
**Replies:** 9\
**Last updated:** [June 16, 2025, 3:27am UTC](https://discourse.slicer.org/t/slicer-wont-create-a-new-database-if-the-path-contains-a-space/43320 "2025-06-16T03:27:46Z")

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When trying to create a DB in which the path contains a folder with a space in the name results in an error message: "Failed to create new database in folder “C:\\Users\\Folder with space\\SlicerDICOMDatabase”. Changing the…

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## [Slices selection in pyradiomics](https://discourse.slicer.org/t/slices-selection-in-pyradiomics/43361)

<div class="topic-metadata">

**Author:** [@iliass\_B25](https://discourse.slicer.org/u/iliass_B25)\
**Replies:** 0\
**Last updated:** [June 15, 2025, 2:34pm UTC](https://discourse.slicer.org/t/slices-selection-in-pyradiomics/43361 "2025-06-15T14:34:10Z")

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I combine the use of SimpleITK with PyRadiomics to extract radiomic features. The thing is, I have a large number of cases, so for the GTV, I take 3 slices above and 3 slices below. Otherwise, the extraction process can …

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## [Slicer Preview upgraded to Python 3.12](https://discourse.slicer.org/t/slicer-preview-upgraded-to-python-3-12/43344)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 1\
**Last updated:** [June 15, 2025, 1:19pm UTC](https://discourse.slicer.org/t/slicer-preview-upgraded-to-python-3-12/43344 "2025-06-15T13:19:53Z")

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Following the integration of PR-8466, Slicer Preview will now provide the Python 3.12 runtime on all supported platforms :rocket: :tada: Thanks everyone who helped support this initiative by providing resources & time …

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## [Torchvision "corrupted" in Pytorch Util](https://discourse.slicer.org/t/torchvision-corrupted-in-pytorch-util/43353)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 3\
**Last updated:** [June 15, 2025, 3:27am UTC](https://discourse.slicer.org/t/torchvision-corrupted-in-pytorch-util/43353 "2025-06-15T03:27:10Z")

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My Pytorch Util module showed TorchVision corrupted I am using Ubuntu 22.04. I have reinstalled pytorch in Pytorch Util multiple times. The Dental Segmentator & Total Segmentator both used the GPU well. nvidia-smi p…

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## [Segmenting average trabecular and cortical volumes of the calvaria](https://discourse.slicer.org/t/segmenting-average-trabecular-and-cortical-volumes-of-the-calvaria/43333)

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**Author:** [@reettak](https://discourse.slicer.org/u/reettak)\
**Replies:** 5\
**Last updated:** [June 14, 2025, 8:57pm UTC](https://discourse.slicer.org/t/segmenting-average-trabecular-and-cortical-volumes-of-the-calvaria/43333 "2025-06-14T20:57:59Z")

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Operating system: win 11 Slicer version: 5.8.1 Expected behavior: Actual behavior: I’ve found myself down a rabbit hole, and I’m looking for opinions/suggestions from more advanced users. Long story short, I would ne…

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## [Error messages showing such as "reference image in series does not contain geometry information. Please use caution.' and ' Could not load: 1000: Key Images as a Scalar Volume'](https://discourse.slicer.org/t/error-messages-showing-such-as-reference-image-in-series-does-not-contain-geometry-information-please-use-caution-and-could-not-load-1000-key-images-as-a-scalar-volume/43354)

<div class="topic-metadata">

**Author:** [@schmacko](https://discourse.slicer.org/u/schmacko)\
**Replies:** 2\
**Last updated:** [June 14, 2025, 6:58am UTC](https://discourse.slicer.org/t/error-messages-showing-such-as-reference-image-in-series-does-not-contain-geometry-information-please-use-caution-and-could-not-load-1000-key-images-as-a-scalar-volume/43354 "2025-06-14T06:58:41Z")

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Hi all, a total newbie here. I’m using 3d slicer to do segmentation of CT scanned images of carotid artery. However, I receive an error message saying ‘reference image in series does not contain geometry information. Ple…

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## [Dicom-seg Export Failure](https://discourse.slicer.org/t/dicom-seg-export-failure/43347)

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**Author:** [@GaryPlayer](https://discourse.slicer.org/u/GaryPlayer)\
**Replies:** 0\
**Last updated:** [June 13, 2025, 8:38pm UTC](https://discourse.slicer.org/t/dicom-seg-export-failure/43347 "2025-06-13T20:38:46Z")

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I am trying to create an example dicom-seg from export. I have my original dicom loaded as a volume and my segmentation (nrrd file) also loaded. Following the tutorial I get the following pop up: So I try and drop …

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## [Undo enabled on an empty segmentation](https://discourse.slicer.org/t/undo-enabled-on-an-empty-segmentation/43332)

<div class="topic-metadata">

**Author:** [@nhjohnston](https://discourse.slicer.org/u/nhjohnston)\
**Replies:** 7\
**Last updated:** [June 13, 2025, 2:32pm UTC](https://discourse.slicer.org/t/undo-enabled-on-an-empty-segmentation/43332 "2025-06-13T14:32:07Z")

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When completing the following steps, the undo/redo buttons are enabled despite no visible changes being made to the segmentation in the scene. Create a new segmentation Select the erase tool Erase in the scene (undo is…

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## [Cranial Implant Reconstruction](https://discourse.slicer.org/t/cranial-implant-reconstruction/43318)

<div class="topic-metadata">

**Author:** [@Alina\_Abbas](https://discourse.slicer.org/u/Alina_Abbas)\
**Replies:** 2\
**Last updated:** [June 13, 2025, 2:19pm UTC](https://discourse.slicer.org/t/cranial-implant-reconstruction/43318 "2025-06-13T14:19:52Z")

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Hello everyone, I hope this message finds you well. I am new to 3D Slicer and am using it for cranial implant reconstruction. I have attempted to utilize the scissor and mirror techniques on my image, but I have not ac…

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## [Can't install Total Segmentor](https://discourse.slicer.org/t/cant-install-total-segmentor/43313)

<div class="topic-metadata">

**Author:** [@kopachini](https://discourse.slicer.org/u/kopachini)\
**Replies:** 3\
**Last updated:** [June 13, 2025, 6:40am UTC](https://discourse.slicer.org/t/cant-install-total-segmentor/43313 "2025-06-13T06:40:17Z")

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Hello everyone. It seems I can’t install Total segmentor. I used it on my older, less powerful laptop but fast version, but now I am not able to install it. This is the error I get. I have Lenovo Legion i9 14900HX …

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