# \#volume

**URL:** https://discourse.slicer.org/tag/volume/45.md

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

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## [Boundary Cut: Upper airway volume + Lower airway volume does not equal Total airway volume](https://discourse.slicer.org/t/boundary-cut-upper-airway-volume-lower-airway-volume-does-not-equal-total-airway-volume/47779)

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**Author:** [@valperrier1999](https://discourse.slicer.org/u/valperrier1999)\
**Replies:** 0\
**Last updated:** [July 31, 2026, 1:37pm UTC](https://discourse.slicer.org/t/boundary-cut-upper-airway-volume-lower-airway-volume-does-not-equal-total-airway-volume/47779 "2026-07-31T13:37:46Z")

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Hello, I am working on a research project where I need to measure upper, lower and total airway volumes from CBCT scans using 3D Slicer (version 5.10.0). My workflow is the following: Segment the complete upper airwa…

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## [Crash when activating "interaction" in subject hierarchy to transform a volume](https://discourse.slicer.org/t/crash-when-activating-interaction-in-subject-hierarchy-to-transform-a-volume/47373)

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**Author:** [@PitaChib](https://discourse.slicer.org/u/PitaChib)\
**Replies:** 2\
**Last updated:** [June 18, 2026, 5:45am UTC](https://discourse.slicer.org/t/crash-when-activating-interaction-in-subject-hierarchy-to-transform-a-volume/47373 "2026-06-18T05:45:50Z")

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I recently updated to Slicer 5.10.0, and today when I load my .nrrd files, a couple times (at least 3 times in the span of finishing 6 scans), I right click to check “interaction” then slicer would just crash and quit. I…

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## [Volume rendering rainbow hue?](https://discourse.slicer.org/t/volume-rendering-rainbow-hue/47319)

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**Author:** [@PitaChib](https://discourse.slicer.org/u/PitaChib)\
**Replies:** 1\
**Last updated:** [June 11, 2026, 5:17pm UTC](https://discourse.slicer.org/t/volume-rendering-rainbow-hue/47319 "2026-06-11T17:17:54Z")

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Hi all, I’m working with a ct scanned skull, and I used the preset microCT bone 16 bit preset to display my volume. However, no matter how I toggle the intensity settings and the advanced things, this hue exists, and as …

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## [Is it possible to rescale intensity of a volume?](https://discourse.slicer.org/t/is-it-possible-to-rescale-intensity-of-a-volume/2543)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 5\
**Last updated:** [May 11, 2026, 7:52pm UTC](https://discourse.slicer.org/t/is-it-possible-to-rescale-intensity-of-a-volume/2543 "2026-05-11T19:52:13Z")

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I want to rescale a Volume created reading a wrongly calibrated dicom file. Is this possible? Usually this is automatically done with the RescaleIntercept and RescaleSlope from the dicom header but when those values are…

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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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## [Link a transform's visibility to transformed volume visibility](https://discourse.slicer.org/t/link-a-transforms-visibility-to-transformed-volume-visibility/45604)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 5\
**Last updated:** [December 31, 2025, 4:19pm UTC](https://discourse.slicer.org/t/link-a-transforms-visibility-to-transformed-volume-visibility/45604 "2025-12-31T16:19:34Z")

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Hi, In my application, I want to load a volume, and give the user controls to spin it around. So when I load the volume, I also create a Transform, make the volume observe it, and then call transformNode.GetDisplayNode(…

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## [Synchronisation window/level across multiple volumes](https://discourse.slicer.org/t/synchronisation-window-level-across-multiple-volumes/45156)

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**Author:** [@ashkanpakzad](https://discourse.slicer.org/u/ashkanpakzad)\
**Replies:** 2\
**Last updated:** [November 21, 2025, 7:41am UTC](https://discourse.slicer.org/t/synchronisation-window-level-across-multiple-volumes/45156 "2025-11-21T07:41:42Z")

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Hi all, I’ve had a search and can’t find much on this. Before I embark on trying to implement this myself, is there an obvious way to link multiple scalar volume nodes window/level, such that if you change the window/le…

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## [Volume calculation of open 3D facial surface models in Slicer](https://discourse.slicer.org/t/volume-calculation-of-open-3d-facial-surface-models-in-slicer/44801)

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**Author:** [@Faisal\_Alshaikh](https://discourse.slicer.org/u/Faisal_Alshaikh)\
**Replies:** 1\
**Last updated:** [October 17, 2025, 6:50pm UTC](https://discourse.slicer.org/t/volume-calculation-of-open-3d-facial-surface-models-in-slicer/44801 "2025-10-17T18:50:08Z")

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Hi, is there any module in 3D Slicer that can calculate the volume of 3D facial surface models (for example .obj files from the Vectra H2 system)? These models are not closed surfaces — for example, they are open at th…

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## [Imported volumes are not aligned](https://discourse.slicer.org/t/imported-volumes-are-not-aligned/42235)

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**Author:** [@Aidan](https://discourse.slicer.org/u/Aidan)\
**Replies:** 4\
**Last updated:** [March 26, 2025, 10:10pm UTC](https://discourse.slicer.org/t/imported-volumes-are-not-aligned/42235 "2025-03-26T22:10:39Z")

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Hi, I have a very basic issue that I can’t seem to figure out. When I import 2 different NIFTI volumes of the same subject from the same session in Slicer (one is an anatomical 3D MR volume and the other is a function EP…

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## [Failure to load RTSTRUCT dicom file](https://discourse.slicer.org/t/failure-to-load-rtstruct-dicom-file/33504)

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**Author:** [@Michele\_R](https://discourse.slicer.org/u/Michele_R)\
**Replies:** 7\
**Last updated:** [December 18, 2024, 10:39am UTC](https://discourse.slicer.org/t/failure-to-load-rtstruct-dicom-file/33504 "2024-12-18T10:39:14Z")

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Operating system: MacOS Ventura Slicer version: 5.7.0 Hello, I am trying to load an image set including a 3D MRI with RT files containing volumetric and dosimetric information that have been exported from a DICOM view…

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## [Why did the segment created by threshold masking contain voxels beyond the threshold?](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123)

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**Author:** [@qmsyylsel](https://discourse.slicer.org/u/qmsyylsel)\
**Replies:** 4\
**Last updated:** [November 15, 2024, 2:32pm UTC](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123 "2024-11-15T14:32:33Z")

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As the pictures shows, in Segment Editor, I painted my segment under the masking with a threshold of \>130. But in Segment Statistics, the minimum value of that segment was 85, which was lower than 130, the threshold I se…

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## [Volume compressed into ROI](https://discourse.slicer.org/t/volume-compressed-into-roi/40085)

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**Author:** [@OwenProulx](https://discourse.slicer.org/u/OwenProulx)\
**Replies:** 12\
**Last updated:** [November 14, 2024, 9:48pm UTC](https://discourse.slicer.org/t/volume-compressed-into-roi/40085 "2024-11-14T21:48:27Z")

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Hi, I’ve been having this issue for a while. I’ve been trying to create an ROI for one of my specimens, and when I load the ROI at full resolution, it instead compresses the whole volume into it, instead of cropping the …

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## [Thick slab reconstruction does not work with MicroCT](https://discourse.slicer.org/t/thick-slab-reconstruction-does-not-work-with-microct/38311)

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**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 2\
**Last updated:** [September 11, 2024, 9:27pm UTC](https://discourse.slicer.org/t/thick-slab-reconstruction-does-not-work-with-microct/38311 "2024-09-11T21:27:54Z")

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Hi all, I noticed when working with MicroCT data that the thick slab reconstruction is not really meant for this modality. The minimum thickness is set to 1mm, which makes it basically unusable for volumes with very sma…

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## [Can you change the dimensions of an image?](https://discourse.slicer.org/t/can-you-change-the-dimensions-of-an-image/38292)

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**Author:** [@Daniel\_Murcia](https://discourse.slicer.org/u/Daniel_Murcia)\
**Replies:** 1\
**Last updated:** [September 9, 2024, 2:30pm UTC](https://discourse.slicer.org/t/can-you-change-the-dimensions-of-an-image/38292 "2024-09-09T14:30:18Z")

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Good morning, dear 3D slicer community. I want to know if the attached values ​​in the image can be changed, if they can I would like to know how to do it. thank you very much for your help.

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## [Segment misalignment](https://discourse.slicer.org/t/segment-misalignment/38003)

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**Author:** [@Arash1](https://discourse.slicer.org/u/Arash1)\
**Replies:** 10\
**Last updated:** [August 30, 2024, 6:05pm UTC](https://discourse.slicer.org/t/segment-misalignment/38003 "2024-08-30T18:05:31Z")

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Hi all Hope you are doing great. I am working on nasal cavity segmentation. One issue that I have is that the segment doesn’t overlap with the DICOM (picture attached). A few technical details to mention are that I di…

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## [Hide a volume programmatically](https://discourse.slicer.org/t/hide-a-volume-programmatically/26654)

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**Author:** [@rhodesdante](https://discourse.slicer.org/u/rhodesdante)\
**Replies:** 9\
**Last updated:** [August 2, 2024, 1:03pm UTC](https://discourse.slicer.org/t/hide-a-volume-programmatically/26654 "2024-08-02T13:03:57Z")

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I am writing a custom module in Python and I would like to: Replace the active volume in the slice viewer (similar to clicking on the “eye” icon of a different volume) with the next volume in the subject hierarchy Shut…

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## [Inquiry about the 'Auto' Control Mode in qMRMLVolumeThresholdWidget](https://discourse.slicer.org/t/inquiry-about-the-auto-control-mode-in-qmrmlvolumethresholdwidget/37232)

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**Author:** [@WilliamDaniel](https://discourse.slicer.org/u/WilliamDaniel)\
**Replies:** 1\
**Last updated:** [July 11, 2024, 4:36am UTC](https://discourse.slicer.org/t/inquiry-about-the-auto-control-mode-in-qmrmlvolumethresholdwidget/37232 "2024-07-11T04:36:37Z")

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Dear 3D Slicer Community, I am a learner of Slicer module development. I am writing to inquire about the underlying principle/algorithm behind the “Auto” option in the Control Mode of the qMRMLVolumeThresholdWidget. …

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## [Combine Multiple Orientations / Volumes in Axial View](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073)

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**Author:** [@waterbottle](https://discourse.slicer.org/u/waterbottle)\
**Replies:** 1\
**Last updated:** [July 8, 2024, 4:33pm UTC](https://discourse.slicer.org/t/combine-multiple-orientations-volumes-in-axial-view/37073 "2024-07-08T16:33:50Z")

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Hi all, Still new to slicer. I am working on MRIs in Slicer. Some MRIs load in as one big volume which works for my needs, however others come split into “imageOrientationPatient X” where X = some number, typically from…

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## [Annotation ROI rotate feature in Volume Reconstruction](https://discourse.slicer.org/t/annotation-roi-rotate-feature-in-volume-reconstruction/36783)

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**Author:** [@MariaGraf](https://discourse.slicer.org/u/MariaGraf)\
**Replies:** 1\
**Last updated:** [June 14, 2024, 2:36pm UTC](https://discourse.slicer.org/t/annotation-roi-rotate-feature-in-volume-reconstruction/36783 "2024-06-14T14:36:55Z")

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I’m working on 3D freehand ultrasounds, creating volumes of muscles. I’ve been told to use the module 'Volume Reconstruction" and when completing the ‘ROI node’ step, the annotationROI is unable to be rotated to adjust f…

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## [Image Position Tag Value different in database and volume node](https://discourse.slicer.org/t/image-position-tag-value-different-in-database-and-volume-node/36039)

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**Author:** [@fqzhice](https://discourse.slicer.org/u/fqzhice)\
**Replies:** 3\
**Last updated:** [May 10, 2024, 1:26pm UTC](https://discourse.slicer.org/t/image-position-tag-value-different-in-database-and-volume-node/36039 "2024-05-10T13:26:20Z")

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Import a CT series to Database, Get image positon tag value in Dicom File Meta data dialog. Then load image in Slicer and check volume info in Volume node, orientation and direction value is different with tag in data ba…

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## [Calculation of Segmentation Volume](https://discourse.slicer.org/t/calculation-of-segmentation-volume/28519)

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**Author:** [@Spiros\_Karkavitsas](https://discourse.slicer.org/u/Spiros_Karkavitsas)\
**Replies:** 3\
**Last updated:** [April 8, 2024, 12:08pm UTC](https://discourse.slicer.org/t/calculation-of-segmentation-volume/28519 "2024-04-08T12:08:01Z")

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Operating system:Windows 10pro Slicer version: Slicer 5.2.1 Hello all I have made some air segmentation of 25 slice dataset. I was wondering if there is an easy way to calculate the volume of the segments. Happy to p…

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## [I want to set the IJK to RAS direction matrix for all my scans I upload. ](https://discourse.slicer.org/t/i-want-to-set-the-ijk-to-ras-direction-matrix-for-all-my-scans-i-upload/34696)

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**Author:** [@Bartdh](https://discourse.slicer.org/u/Bartdh)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 8:27pm UTC](https://discourse.slicer.org/t/i-want-to-set-the-ijk-to-ras-direction-matrix-for-all-my-scans-i-upload/34696 "2024-03-04T20:27:14Z")

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I want to set the IJK to RAS direction matrix for all my scans I upload. The current matrix gives me a mirrored volume after segmentation. I believe the “IJK to RAS direction matrix” should be (1 0 0, 0 1 0, 0 0 1). How …

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## [3D Ultrasound Reconstruction with openIGTL (Verasonics & Polhemus)](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240)

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**Author:** [@ehdrmfdl3648](https://discourse.slicer.org/u/ehdrmfdl3648)\
**Replies:** 8\
**Last updated:** [February 22, 2024, 12:59am UTC](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240 "2024-02-22T00:59:34Z")

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US img: Verasonics 64 LE Position Sensor: Polhemus EMT Sensor Here’s what’s going on made Verasonics’ images available for import in Python. the values of the EMT sensor were imported into Python and a transform …

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## [Pixel Spacing for volume reconstruction of ultrasound images](https://discourse.slicer.org/t/pixel-spacing-for-volume-reconstruction-of-ultrasound-images/33311)

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**Author:** [@Pratima](https://discourse.slicer.org/u/Pratima)\
**Replies:** 2\
**Last updated:** [December 9, 2023, 5:06pm UTC](https://discourse.slicer.org/t/pixel-spacing-for-volume-reconstruction-of-ultrasound-images/33311 "2023-12-09T17:06:00Z")

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Hello I am new to 3D slicer.I have a telemed C5-2R60S-3 potable ultrasound probe and windows 11 Pro.I want to scan the abdomen and generate 3d volume.I have used plusApp & Slicer openIGTlinkIF to successfully visualize …

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## [Adjusting margin sizes based on volume ratios and axes](https://discourse.slicer.org/t/adjusting-margin-sizes-based-on-volume-ratios-and-axes/32974)

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**Author:** [@ally7113](https://discourse.slicer.org/u/ally7113)\
**Replies:** 1\
**Last updated:** [November 23, 2023, 9:01pm UTC](https://discourse.slicer.org/t/adjusting-margin-sizes-based-on-volume-ratios-and-axes/32974 "2023-11-23T21:01:43Z")

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Sorry for the low-quality image… I would like to expand the existing segment in three directions based on the volume ratio. For instance, I want to expand by 5% along the x-axis, 10% along the y-axis, and 10% along t…

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## [Distorted & malaligned volumes after loading DICOM sets](https://discourse.slicer.org/t/distorted-malaligned-volumes-after-loading-dicom-sets/26088)

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**Author:** [@MCM-Fischer](https://discourse.slicer.org/u/MCM-Fischer)\
**Replies:** 12\
**Last updated:** [November 13, 2023, 8:38am UTC](https://discourse.slicer.org/t/distorted-malaligned-volumes-after-loading-dicom-sets/26088 "2023-11-13T08:38:53Z")

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Hello I’ve got multiple DICOM datasets that are not properly loaded by Slicer. The volumes are distorted and are incorrectly aligned to each other. The distortion is caused by an incorrect scaling along the superoinfe…

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## [Merge Models with Volume](https://discourse.slicer.org/t/merge-models-with-volume/31937)

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**Author:** [@Bahram\_Zargar](https://discourse.slicer.org/u/Bahram_Zargar)\
**Replies:** 3\
**Last updated:** [September 28, 2023, 2:51am UTC](https://discourse.slicer.org/t/merge-models-with-volume/31937 "2023-09-28T02:51:44Z")

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3d Slicer version 5.2.2 OS: Linux Redhat 8 Hello 3D slicer experts, I do have an MRI volume, with 6 models in my 3D Slicer, and can export each of them separately as DICOM file. However what I want to do is to merge a…

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## [Obtaining Volume Information for Brain Segmentation Using Closed-Loop Markups in 3D Slicer](https://discourse.slicer.org/t/obtaining-volume-information-for-brain-segmentation-using-closed-loop-markups-in-3d-slicer/31846)

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**Author:** [@sund](https://discourse.slicer.org/u/sund)\
**Replies:** 1\
**Last updated:** [September 22, 2023, 3:36pm UTC](https://discourse.slicer.org/t/obtaining-volume-information-for-brain-segmentation-using-closed-loop-markups-in-3d-slicer/31846 "2023-09-22T15:36:35Z")

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Hello everyone, I have been using the closed-loop markup module in 3D Slicer to segment the brain on individual MRI slices. Now, I am trying to obtain volume information for the entire brain by considering the closed-lo…

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## [Volume rendering gives solid box despite working XYZ views and adjusting preset/shift](https://discourse.slicer.org/t/volume-rendering-gives-solid-box-despite-working-xyz-views-and-adjusting-preset-shift/31775)

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**Author:** [@shika](https://discourse.slicer.org/u/shika)\
**Replies:** 4\
**Last updated:** [September 19, 2023, 9:44pm UTC](https://discourse.slicer.org/t/volume-rendering-gives-solid-box-despite-working-xyz-views-and-adjusting-preset-shift/31775 "2023-09-19T21:44:17Z")

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Hello there, I am a new user of Slicer but I have read through the wiki and other related help forums. I have been having issues with rendering from a stack of images, specifically using the SlicerMorph ImageStacks util…

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## [Volume and minimal cross section areas in the nasal cavity](https://discourse.slicer.org/t/volume-and-minimal-cross-section-areas-in-the-nasal-cavity/29377)

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**Author:** [@AKue](https://discourse.slicer.org/u/AKue)\
**Replies:** 5\
**Last updated:** [May 31, 2023, 2:32pm UTC](https://discourse.slicer.org/t/volume-and-minimal-cross-section-areas-in-the-nasal-cavity/29377 "2023-05-31T14:32:11Z")

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Hello! I would like to segment the nasal cavity with the aim to get: the total volume of the whole nasal cavity the volume of different parts of the nasal cavity the minimal cross section areas of the right and the lef…

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