# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=14

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

**Page:** 15

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## [Brain Tissues Extension not found/Separating Brain Tissues](https://discourse.slicer.org/t/brain-tissues-extension-not-found-separating-brain-tissues/15427)

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**Author:** [@Miguel](https://discourse.slicer.org/u/Miguel)\
**Replies:** 1\
**Last updated:** [February 17, 2026, 8:55am UTC](https://discourse.slicer.org/t/brain-tissues-extension-not-found-separating-brain-tissues/15427 "2026-02-17T08:55:09Z")

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Hello all, I need to separate gray and white matter and CSF from a volume, but I cannot find the BrainTissuesExtension. I am new here so I don’t know if there is an efficient way to segment it, or how can I install it. …

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## [Generate a 3d model/point cloud from CT scan of abdomen](https://discourse.slicer.org/t/generate-a-3d-model-point-cloud-from-ct-scan-of-abdomen/34842)

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**Author:** [@Pratima](https://discourse.slicer.org/u/Pratima)\
**Replies:** 2\
**Last updated:** [February 17, 2026, 8:37am UTC](https://discourse.slicer.org/t/generate-a-3d-model-point-cloud-from-ct-scan-of-abdomen/34842 "2026-02-17T08:37:25Z")

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Hello, I want to know step-by-step process on how to convert and download a segmented CT scan model (visible in Slicer) into Point Cloud/STL format. I am a beginner in 3D slicing. Any help is highly appreciated.

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## [endless loading in the dental segmentator](https://discourse.slicer.org/t/endless-loading-in-the-dental-segmentator/46178)

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**Author:** [@Imran](https://discourse.slicer.org/u/Imran)\
**Replies:** 0\
**Last updated:** [February 16, 2026, 4:51pm UTC](https://discourse.slicer.org/t/endless-loading-in-the-dental-segmentator/46178 "2026-02-16T16:51:15Z")

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I installed the dental segmentator extension to automatically segment the cbct. I download the cbct, click apply, and the download begins, which lasts indefinitely. nvidia rtx 4070 gpu. help me fix it

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## [Generate segmentation node (binary label map) from centerline](https://discourse.slicer.org/t/generate-segmentation-node-binary-label-map-from-centerline/26166)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 5\
**Last updated:** [February 16, 2026, 1:03am UTC](https://discourse.slicer.org/t/generate-segmentation-node-binary-label-map-from-centerline/26166 "2026-02-16T01:03:58Z")

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Hi, I want to obtain a label map corresponding to centerline generated by VMTK. I would also like to get a different label for voxels belonging to different branches. I have generated centerline tree for a vessel label…

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## [SlicerIGT U37 Neuronav Error](https://discourse.slicer.org/t/slicerigt-u37-neuronav-error/44106)

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**Author:** [@coldfire85](https://discourse.slicer.org/u/coldfire85)\
**Replies:** 2\
**Last updated:** [February 15, 2026, 6:14pm UTC](https://discourse.slicer.org/t/slicerigt-u37-neuronav-error/44106 "2026-02-15T18:14:25Z")

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IM trying to follow the tutorial from Neuronav ppt but i run into this error - \[VTK\] Warning: In vtkMRMLMarkupsFiducialNode.h, line 113 \[VTK\] vtkMRMLMarkupsFiducialNode (0000029120E822D0): vtkMRMLMarkupsFiducialNode::A…

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## [Modul GPA, Interactive 3D Visualization, PCA Visualization Parameters slider](https://discourse.slicer.org/t/modul-gpa-interactive-3d-visualization-pca-visualization-parameters-slider/46149)

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**Author:** [@juliangallaun](https://discourse.slicer.org/u/juliangallaun)\
**Replies:** 2\
**Last updated:** [February 15, 2026, 2:27pm UTC](https://discourse.slicer.org/t/modul-gpa-interactive-3d-visualization-pca-visualization-parameters-slider/46149 "2026-02-15T14:27:08Z")

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Hello all, I have a logical question regarding the slider increments and their relation to let’s say my PC1 axis. I did 2D morphometric analysis in other programs (Thin plate spline) and let’s say my sample with highe…

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## [Problem with TotalSegmentator - my computer freezes](https://discourse.slicer.org/t/problem-with-totalsegmentator-my-computer-freezes/46068)

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**Author:** [@jimenagonzalezsal](https://discourse.slicer.org/u/jimenagonzalezsal)\
**Replies:** 2\
**Last updated:** [February 15, 2026, 2:08pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator-my-computer-freezes/46068 "2026-02-15T14:08:29Z")

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Hello! I need help. I’m trying to segment lumbar spine DICOMs, but whenever I click Apply, my computer freezes and the segmentation never finishes.

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## [Unable to add DICOM data](https://discourse.slicer.org/t/unable-to-add-dicom-data/46156)

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**Author:** [@Akash\_Raj\_G\_P](https://discourse.slicer.org/u/Akash_Raj_G_P)\
**Replies:** 2\
**Last updated:** [February 14, 2026, 3:38pm UTC](https://discourse.slicer.org/t/unable-to-add-dicom-data/46156 "2026-02-14T15:38:56Z")

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When I click on the ‘Add DICOM data’ button on the homepage I get an error message that says ‘Unfortunately this requested module is not available in this Slicer session‘. I have not seen this error occur for anybody els…

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## [Brain Modelling](https://discourse.slicer.org/t/brain-modelling/46154)

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**Author:** [@nakcali](https://discourse.slicer.org/u/nakcali)\
**Replies:** 2\
**Last updated:** [February 14, 2026, 3:36pm UTC](https://discourse.slicer.org/t/brain-modelling/46154 "2026-02-14T15:36:52Z")

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Hello, Can someone help me? I am trying to create a 3D model of my brain. I am using Swiss Skull Stripper, but I am not able to do it properly. It looks like lego brain. My MRI data seem to be divided into several grou…

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## [3d slicer and totalsegmentator in mac](https://discourse.slicer.org/t/3d-slicer-and-totalsegmentator-in-mac/46135)

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**Author:** [@alex\_He](https://discourse.slicer.org/u/alex_He)\
**Replies:** 1\
**Last updated:** [February 14, 2026, 5:17am UTC](https://discourse.slicer.org/t/3d-slicer-and-totalsegmentator-in-mac/46135 "2026-02-14T05:17:53Z")

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I have installed 3d slicer 5. 10 in mac mini. I also installed laterest totalsegmentator using slicer extension. But when I apply the error message torch not found occur. Is there something I should take note when using …

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## [Calculating difference in dose between two CT scans](https://discourse.slicer.org/t/calculating-difference-in-dose-between-two-ct-scans/46047)

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**Author:** [@hanginghats](https://discourse.slicer.org/u/hanginghats)\
**Replies:** 3\
**Last updated:** [February 14, 2026, 5:11am UTC](https://discourse.slicer.org/t/calculating-difference-in-dose-between-two-ct-scans/46047 "2026-02-14T05:11:02Z")

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I’m doing a project which requires me to analyse the difference in dose between two identical CT scans reconstructed with different algorithms. Is there any way for me to do this with slicer and slicerRT?

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## [Guidance on Intensity Correction for Siemens Multiband EPI Data](https://discourse.slicer.org/t/guidance-on-intensity-correction-for-siemens-multiband-epi-data/46155)

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**Author:** [@Muhammad\_Faizan](https://discourse.slicer.org/u/Muhammad_Faizan)\
**Replies:** 1\
**Last updated:** [February 14, 2026, 4:56am UTC](https://discourse.slicer.org/t/guidance-on-intensity-correction-for-siemens-multiband-epi-data/46155 "2026-02-14T04:56:26Z")

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I am working with EPI d ata acquired on a Siemens 3T scanner. The data is multiband with no in-plane acceleration. I reconstructed the multiband data using the slice GRAPPA technique. However, I am facing an issue: …

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## [Markups misalignment with the volume](https://discourse.slicer.org/t/markups-misalignment-with-the-volume/46137)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 1\
**Last updated:** [February 14, 2026, 4:47am UTC](https://discourse.slicer.org/t/markups-misalignment-with-the-volume/46137 "2026-02-14T04:47:56Z")

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Hi to everyone. I’m using this script to extract the pointCloud positions in IJK system: def RAStoIJK(xyz, volumeNode, RAS = True): """ Transforms a list of points or np array of shape (n,3) in RAS coordinates …

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## [Data Load Failed](https://discourse.slicer.org/t/data-load-failed/46144)

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**Author:** [@Daniel\_C](https://discourse.slicer.org/u/Daniel_C)\
**Replies:** 3\
**Last updated:** [February 13, 2026, 7:04pm UTC](https://discourse.slicer.org/t/data-load-failed/46144 "2026-02-13T19:04:42Z")

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Hi there, I encountered an error while trying to open a set of CT TIFF images. The error message only shows “load failed.” Is there any way to resolve this issue?

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## [How to use the PySERA in 3D Slicer?](https://discourse.slicer.org/t/how-to-use-the-pysera-in-3d-slicer/46133)

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**Author:** [@Subhash\_Kheruka](https://discourse.slicer.org/u/Subhash_Kheruka)\
**Replies:** 0\
**Last updated:** [February 12, 2026, 7:07am UTC](https://discourse.slicer.org/t/how-to-use-the-pysera-in-3d-slicer/46133 "2026-02-12T07:07:29Z")

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I want to know how to install the pysera in 3 D slicer

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## [3D slicer 5.10 SlicerSPECTRecon Critical warning: this will cause errors after 2025-11-30](https://discourse.slicer.org/t/3d-slicer-5-10-slicerspectrecon-critical-warning-this-will-cause-errors-after-2025-11-30/46132)

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**Author:** [@macp970617](https://discourse.slicer.org/u/macp970617)\
**Replies:** 0\
**Last updated:** [February 12, 2026, 7:06am UTC](https://discourse.slicer.org/t/3d-slicer-5-10-slicerspectrecon-critical-warning-this-will-cause-errors-after-2025-11-30/46132 "2026-02-12T07:06:14Z")

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Applications/Slicer.app/Contents/Extensions-34045/SPECTRecon/lib/Slicer-5.10/qt-scripted-modules/SPECTRecon.py:3: UserWarning: pkg\_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg\_resources…

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## [Segmenting only within a ROI](https://discourse.slicer.org/t/segmenting-only-within-a-roi/46129)

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**Author:** [@jamie.miller.phd](https://discourse.slicer.org/u/jamie.miller.phd)\
**Replies:** 0\
**Last updated:** [February 12, 2026, 7:05am UTC](https://discourse.slicer.org/t/segmenting-only-within-a-roi/46129 "2026-02-12T07:05:17Z")

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Hi team, I am a novice user of 3D Slicer and trying to upskill. I have MRI images of the upper airway and I am trying to segment out only the airways (nasal and oral cavities). I have been using the threshold masking to …

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## [3D Slicer does not start as full screen](https://discourse.slicer.org/t/3d-slicer-does-not-start-as-full-screen/46122)

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**Author:** [@strider\_hunter](https://discourse.slicer.org/u/strider_hunter)\
**Replies:** 0\
**Last updated:** [February 11, 2026, 8:39am UTC](https://discourse.slicer.org/t/3d-slicer-does-not-start-as-full-screen/46122 "2026-02-11T08:39:38Z")

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When I startup up 3D Slicer, instead of occupying the full screen, it only occupies a smaller section (as seen in the screenshot below). I have a multi-monitor setup. I looked at a \`.ini\` files like slicer.org\\Slicer-…

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## [Breast PET/CT segmentation](https://discourse.slicer.org/t/breast-pet-ct-segmentation/46116)

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**Author:** [@Issa\_Abusaleh](https://discourse.slicer.org/u/Issa_Abusaleh)\
**Replies:** 1\
**Last updated:** [February 10, 2026, 9:16pm UTC](https://discourse.slicer.org/t/breast-pet-ct-segmentation/46116 "2026-02-10T21:16:38Z")

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I am writing to kindly request your guidance and support in learning segmentation techniques step by step, as I am currently working on a research project entitled: “PET/CT Predicting Treatment Response of Breast Cancer…

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## [Mimics to Slicer Masks and Models - Pre-Tracking Segmentation](https://discourse.slicer.org/t/mimics-to-slicer-masks-and-models-pre-tracking-segmentation/46111)

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**Author:** [@Shilpa\_Rao](https://discourse.slicer.org/u/Shilpa_Rao)\
**Replies:** 1\
**Last updated:** [February 10, 2026, 4:17pm UTC](https://discourse.slicer.org/t/mimics-to-slicer-masks-and-models-pre-tracking-segmentation/46111 "2026-02-10T16:17:36Z")

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I’m trying to repeat segmentation workflows from Mimics to Slicer, with the end-goal being tracking. In Mimics, there is a distinction between masks and models, where models are exported as VRML 2.0 files (then converte…

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## [Can you erase something in the sagittal plane, without affecting segmentations made in the axial plane?](https://discourse.slicer.org/t/can-you-erase-something-in-the-sagittal-plane-without-affecting-segmentations-made-in-the-axial-plane/46112)

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**Author:** [@Severin](https://discourse.slicer.org/u/Severin)\
**Replies:** 1\
**Last updated:** [February 10, 2026, 3:51pm UTC](https://discourse.slicer.org/t/can-you-erase-something-in-the-sagittal-plane-without-affecting-segmentations-made-in-the-axial-plane/46112 "2026-02-10T15:51:34Z")

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Hello everyone, My apologies, probably this has already been addressed previously and I am just not able to find the answer. I am using Slicer 3D (5.8) with Biomedisa and segmented every 20th slice in the axial plane. …

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## [How to overlay pre- and post-operative dental DICOM files to measure bone gain ?](https://discourse.slicer.org/t/how-to-overlay-pre-and-post-operative-dental-dicom-files-to-measure-bone-gain/46099)

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**Author:** [@Sont](https://discourse.slicer.org/u/Sont)\
**Replies:** 3\
**Last updated:** [February 10, 2026, 12:50pm UTC](https://discourse.slicer.org/t/how-to-overlay-pre-and-post-operative-dental-dicom-files-to-measure-bone-gain/46099 "2026-02-10T12:50:25Z")

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Hello, I would like to overlay two dental DICOM files (pre-operative and post-operative) following a bone graft in order to measure the volumetric bone gain (in mm and/or %). To perform these measurements, I would need …

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## [Strategies for working with large microCT files](https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847)

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**Author:** [@Antmaker](https://discourse.slicer.org/u/Antmaker)\
**Replies:** 6\
**Last updated:** [February 10, 2026, 12:18am UTC](https://discourse.slicer.org/t/strategies-for-working-with-large-microct-files/45847 "2026-02-10T00:18:36Z")

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Hi, I am working with microCT tiff stacks and currently it is 75GB when read into the software at full resolution. Following the general guideline of using a hardware with RAM 6x-10x that of the file is not attainable e…

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## [ADC images Quantifications ](https://discourse.slicer.org/t/adc-images-quantifications/46074)

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**Author:** [@a.altairan](https://discourse.slicer.org/u/a.altairan)\
**Replies:** 3\
**Last updated:** [February 9, 2026, 11:08pm UTC](https://discourse.slicer.org/t/adc-images-quantifications/46074 "2026-02-09T23:08:52Z")

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hello everyone I’m doing study involving Lumber spine, I’m trying to calculate the ADC mean and median values but I’m getting values with ( - ), how to overcome this issue ?

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## [DeCAL producing weird clustering of landmarks](https://discourse.slicer.org/t/decal-producing-weird-clustering-of-landmarks/46071)

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**Author:** [@raranda22](https://discourse.slicer.org/u/raranda22)\
**Replies:** 3\
**Last updated:** [February 9, 2026, 6:31pm UTC](https://discourse.slicer.org/t/decal-producing-weird-clustering-of-landmarks/46071 "2026-02-09T18:31:04Z")

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Hello, I have run DeCAL many times with a handful of meshes and curve semilandmarks from the MarkMyBird dataset. Each time, some of the surface landmarks cluster very closely together in strange ways. I would expect the…

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## [Issues with scaling information added to .tiff volume- tried ImageStacks and saving as .nrrd?](https://discourse.slicer.org/t/issues-with-scaling-information-added-to-tiff-volume-tried-imagestacks-and-saving-as-nrrd/46084)

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**Author:** [@alsig](https://discourse.slicer.org/u/alsig)\
**Replies:** 10\
**Last updated:** [February 9, 2026, 12:10am UTC](https://discourse.slicer.org/t/issues-with-scaling-information-added-to-tiff-volume-tried-imagestacks-and-saving-as-nrrd/46084 "2026-02-09T00:10:01Z")

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Hi everyone, I am having a issue when trying to import/save TIFF data in a way that lets me add the scaling information. I have a single file ImageJ hyperstack .tiff that has my entire volume, with X-Y scale of 0.00128…

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## [Clinical DICOM loading error, PixelData larger than remaining bytes in file, but images look OK](https://discourse.slicer.org/t/clinical-dicom-loading-error-pixeldata-larger-than-remaining-bytes-in-file-but-images-look-ok/46077)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [February 8, 2026, 10:44pm UTC](https://discourse.slicer.org/t/clinical-dicom-loading-error-pixeldata-larger-than-remaining-bytes-in-file-but-images-look-ok/46077 "2026-02-08T22:44:20Z")

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When I download an image series directly from our clinical PACS and import it into Slicer, I get the following error message repeated for each .dcm file: “E: DcmElement: PixelData (7fe0,0010) larger (4294967295) than re…

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## [Can beam hardening artefact be turned into a real looking vessel](https://discourse.slicer.org/t/can-beam-hardening-artefact-be-turned-into-a-real-looking-vessel/46085)

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**Author:** [@Vonni3](https://discourse.slicer.org/u/Vonni3)\
**Replies:** 6\
**Last updated:** [February 8, 2026, 8:15pm UTC](https://discourse.slicer.org/t/can-beam-hardening-artefact-be-turned-into-a-real-looking-vessel/46085 "2026-02-08T20:15:01Z")

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Hello I have what looks like connections from Superior Vena Cava to Aorta. They look real, but are they? They have vessel walls and curve.

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## [MONAI Auto3DSeg – inconsistent performance for vertebral body segmentation](https://discourse.slicer.org/t/monai-auto3dseg-inconsistent-performance-for-vertebral-body-segmentation/46081)

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**Author:** [@jchao](https://discourse.slicer.org/u/jchao)\
**Replies:** 1\
**Last updated:** [February 8, 2026, 4:31pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-inconsistent-performance-for-vertebral-body-segmentation/46081 "2026-02-08T16:31:36Z")

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Hi everyone, I’m currently working with Prof. Ron Alkalay on a spine CT segmentation project using MONAI Auto3DSeg and would appreciate any advice from the community. My task is to segment only vertebral bodies. I refo…

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## [Surface model turns black under transformation](https://discourse.slicer.org/t/surface-model-turns-black-under-transformation/46065)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [February 5, 2026, 7:01pm UTC](https://discourse.slicer.org/t/surface-model-turns-black-under-transformation/46065 "2026-02-05T19:01:19Z")

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When I reflect a model node using a linear transform node that has a reflection, the visualization of it in 3D unexpectedly turns black. I gather from other posts and LLM consultation that this is because a transform wi…

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