# \#cropping **URL:** https://discourse.slicer.org/tag/cropping/278.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [data disappearing after crop volume](https://discourse.slicer.org/t/data-disappearing-after-crop-volume/46467)
**Author:** [@fergu365](https://discourse.slicer.org/u/fergu365)\ **Replies:** 1\ **Last updated:** [March 16, 2026, 7:38pm UTC](https://discourse.slicer.org/t/data-disappearing-after-crop-volume/46467 "2026-03-16T19:38:09Z")
Every time I attempt to make on ROI and then crop volume, once I hit apply, all the CT data disappears. It’s not just the data outside the ROI (that would make sense), it is the entire scan. I’ve tried to troubleshoot by… --- ## [Crop Volume module returning empty volume](https://discourse.slicer.org/t/crop-volume-module-returning-empty-volume/40323)
**Author:** [@Dboerma](https://discourse.slicer.org/u/Dboerma)\ **Replies:** 1\ **Last updated:** [November 21, 2024, 10:25pm UTC](https://discourse.slicer.org/t/crop-volume-module-returning-empty-volume/40323 "2024-11-21T22:25:39Z")
Hello Slicer team! OS: Windows 10 (22H2) Slicer Version: 5.6.2 RAM: 128 GB Data: DICOMs (12.4 GB) Expected Behavior: When using an ROI to define a cropping region (both in the Crop Volumes module and when using the … --- ## [Two markupsROI (Cropping module)](https://discourse.slicer.org/t/two-markupsroi-cropping-module/39956)
**Author:** [@Dawid\_Szczawinski](https://discourse.slicer.org/u/Dawid_Szczawinski)\ **Replies:** 2\ **Last updated:** [October 31, 2024, 4:24pm UTC](https://discourse.slicer.org/t/two-markupsroi-cropping-module/39956 "2024-10-31T16:24:46Z")
Hello everyone! I try to create my own extension to using nnunetv2 model. First step is cropping data, because segmentation full file is not necessary and I have too little ram. So I try to cropp Volume using ROI. Is… --- ## [Nasal Cavity Segmentation](https://discourse.slicer.org/t/nasal-cavity-segmentation/38219)
**Author:** [@Arash1](https://discourse.slicer.org/u/Arash1)\ **Replies:** 0\ **Last updated:** [September 4, 2024, 8:27pm UTC](https://discourse.slicer.org/t/nasal-cavity-segmentation/38219 "2024-09-04T20:27:23Z")
Hello I wanted to ask for advice on nasal cavity segmentation. (turbinates and sinuses). I have my CT Scan dataset and have resampled it, which has helped a lot. Using the threshold, level tracing, paint, erase, and l… --- ## [Segment misalignment](https://discourse.slicer.org/t/segment-misalignment/38003)
**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")
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… --- ## [Crop Volume Not Working](https://discourse.slicer.org/t/crop-volume-not-working/38067)
**Author:** [@Arash1](https://discourse.slicer.org/u/Arash1)\ **Replies:** 3\ **Last updated:** [August 30, 2024, 10:25am UTC](https://discourse.slicer.org/t/crop-volume-not-working/38067 "2024-08-30T10:25:20Z")
Hi I have an issue that I dont know the reason. No new modules was installed, dataset are the same, and pretty much everything but the Crop Volume module is not working. Here are the codes Python 3.9.10 (main, Apr 5 … --- ## [How to crop a segmentation?](https://discourse.slicer.org/t/how-to-crop-a-segmentation/34408)
**Author:** [@harad](https://discourse.slicer.org/u/harad)\ **Replies:** 4\ **Last updated:** [February 20, 2024, 9:11am UTC](https://discourse.slicer.org/t/how-to-crop-a-segmentation/34408 "2024-02-20T09:11:47Z")
I need the tumor segmentation exported as a separate, standalone DICOM file. This cannot be done by crop volume because only rectangular shapes can be cropped in this way. All attempts to export a segmentation end up onl… --- ## [Issue with Volume Cropping](https://discourse.slicer.org/t/issue-with-volume-cropping/34335)
**Author:** [@joseph00](https://discourse.slicer.org/u/joseph00)\ **Replies:** 3\ **Last updated:** [February 15, 2024, 7:09am UTC](https://discourse.slicer.org/t/issue-with-volume-cropping/34335 "2024-02-15T07:09:45Z")
Hello everyone, I am encountering an issue with the volume cropping functionality in 3D Slicer and would greatly appreciate any assistance or guidance you could provide. When attempting to perform a volume crop Volume … --- ## [Cropping existing volume with ROI and shifting display via Python scripting](https://discourse.slicer.org/t/cropping-existing-volume-with-roi-and-shifting-display-via-python-scripting/33856)
**Author:** [@paleomariomm](https://discourse.slicer.org/u/paleomariomm)\ **Replies:** 4\ **Last updated:** [January 19, 2024, 5:37pm UTC](https://discourse.slicer.org/t/cropping-existing-volume-with-roi-and-shifting-display-via-python-scripting/33856 "2024-01-19T17:37:04Z")
Hi community. I am writing a Python script to automate a pipeline that will be used in around 1000 CT scans. Now I am able to load 1 DICOM folder and to display Volume rendering with Python # Load DICOM files # https… --- ## [Using interpolation when cropping volume](https://discourse.slicer.org/t/using-interpolation-when-cropping-volume/33712)
**Author:** [@rsalkin](https://discourse.slicer.org/u/rsalkin)\ **Replies:** 3\ **Last updated:** [January 11, 2024, 7:23pm UTC](https://discourse.slicer.org/t/using-interpolation-when-cropping-volume/33712 "2024-01-11T19:23:24Z")
Hello, I am currently using the cropping feature (converters → crop volume) to select a specific ROI on lung CTs. Using the cropping bounding box, I also crop binary tumor segmentations (read as volumes). The “interpola… --- ## [How to clean up temp file after cropping volume](https://discourse.slicer.org/t/how-to-clean-up-temp-file-after-cropping-volume/12939)
**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\ **Replies:** 4\ **Last updated:** [August 11, 2020, 4:44am UTC](https://discourse.slicer.org/t/how-to-clean-up-temp-file-after-cropping-volume/12939 "2020-08-11T04:44:12Z")
Hi, I have a script that automatically crops (and resamples) my volumes in Slicer. It works fine, but every time it runs, it leaves a copy of the original volume in the temp folder. In my case, here: c:\\Users\\tamas\\App… --- ## [Crop volume python script](https://discourse.slicer.org/t/crop-volume-python-script/30034)
**Author:** [@Mani\_Barathi](https://discourse.slicer.org/u/Mani_Barathi)\ **Replies:** 5\ **Last updated:** [June 28, 2023, 3:10am UTC](https://discourse.slicer.org/t/crop-volume-python-script/30034 "2023-06-28T03:10:43Z")
Please help me with the python scripting for crop volume to crop the brain? --- ## [Nearest Neighbor implementation](https://discourse.slicer.org/t/nearest-neighbor-implementation/29529)
**Author:** [@osmandogan](https://discourse.slicer.org/u/osmandogan)\ **Replies:** 2\ **Last updated:** [May 18, 2023, 10:23pm UTC](https://discourse.slicer.org/t/nearest-neighbor-implementation/29529 "2023-05-18T22:23:22Z")
Hello. I am doing a volume crop operation in a study I have been working on. And I want to use the “Nearest Neighborn” feature from the interpolator features in the “Volume Crop” module. How can I add the “Nearest Neighb… --- ## [Uncapped Cropped Parts in 3D View](https://discourse.slicer.org/t/uncapped-cropped-parts-in-3d-view/28525)
**Author:** [@SassanHashemi](https://discourse.slicer.org/u/SassanHashemi)\ **Replies:** 0\ **Last updated:** [March 22, 2023, 4:17pm UTC](https://discourse.slicer.org/t/uncapped-cropped-parts-in-3d-view/28525 "2023-03-22T16:17:42Z")
Hello Slicer community, I don’t know if there is a workaround for this or not, but I wanted to see if there is a way to “cap” the cropped parts along the cropping plane? As you can see in the video, it makes… --- ## [ROI cropping and segmentation](https://discourse.slicer.org/t/roi-cropping-and-segmentation/28434)
**Author:** [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\ **Replies:** 1\ **Last updated:** [March 18, 2023, 8:11pm UTC](https://discourse.slicer.org/t/roi-cropping-and-segmentation/28434 "2023-03-18T20:11:31Z")
Hi, In case of feature extraction from ct images and for any analysis such as prediction, should we crop then segment ROI or just segmentation is enough? Prof @lassoan,@rbumm I would appreciate if you share your opinio… --- ## [Volume cropping CT images using lung masks](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155)
**Author:** [@Vahdane](https://discourse.slicer.org/u/Vahdane)\ **Replies:** 2\ **Last updated:** [March 3, 2023, 2:58pm UTC](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155 "2023-03-03T14:58:55Z")
Hello, I want to crop the lung CT image to lobe subregions by using lung masks. I have the masks, however, as far as I know, we can only crop the image to a rectangular shape in the crop volume module. Thanks for your … --- ## [Resize an image by averaging?](https://discourse.slicer.org/t/resize-an-image-by-averaging/24565)
**Author:** [@drakewilliams](https://discourse.slicer.org/u/drakewilliams)\ **Replies:** 2\ **Last updated:** [July 29, 2022, 6:03pm UTC](https://discourse.slicer.org/t/resize-an-image-by-averaging/24565 "2022-07-29T18:03:22Z")
Hi, I’m working with microct images (animal) and we typically only need a small area (teeth) for analysis even though we have a much larger volume scanned (whole skull). My computer is underpowered to load the whole sku… --- ## [combine two volumes into one using python](https://discourse.slicer.org/t/combine-two-volumes-into-one-using-python/23152)
**Author:** [@Katya\_Stansfield](https://discourse.slicer.org/u/Katya_Stansfield)\ **Replies:** 8\ **Last updated:** [April 29, 2022, 8:17am UTC](https://discourse.slicer.org/t/combine-two-volumes-into-one-using-python/23152 "2022-04-29T08:17:14Z")
Hi, I need to automate combining two volumes into one. I have DICOM files of whole body CT scans of a body, split into parts. The parts overlap slightly. My aim is to be able to quickly merge the torso and legs to obtain… --- ## [Show changes in Crop Volume interface](https://discourse.slicer.org/t/show-changes-in-crop-volume-interface/21250)
**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\ **Replies:** 2\ **Last updated:** [December 30, 2021, 9:49am UTC](https://discourse.slicer.org/t/show-changes-in-crop-volume-interface/21250 "2021-12-30T09:49:21Z")
Hi all, I am writing my own code to crop a volume. What I have is: #Input volume slicer.util.selectModule('CropVolume') cropVolumeNode = slicer.vtkMRMLCropVolumeParametersNode() cropVolumeNode.SetScene(slicer.mrmlScene… --- ## [Fix size in cropped volume](https://discourse.slicer.org/t/fix-size-in-cropped-volume/21114)
**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\ **Replies:** 7\ **Last updated:** [December 20, 2021, 9:37pm UTC](https://discourse.slicer.org/t/fix-size-in-cropped-volume/21114 "2021-12-20T21:37:49Z")
Hi, I want to crop a volume with a fixed size, let’s say 400x400. As far as I know, there is no way to set the dimension of the AnnotationROI in Crop Volume module. (I can do it manually but it’s quite frustrating). Is… --- ## [Python: Programmatically set the Dimensions for ROI](https://discourse.slicer.org/t/python-programmatically-set-the-dimensions-for-roi/18817)
**Author:** [@Panda](https://discourse.slicer.org/u/Panda)\ **Replies:** 1\ **Last updated:** [August 3, 2021, 5:42pm UTC](https://discourse.slicer.org/t/python-programmatically-set-the-dimensions-for-roi/18817 "2021-08-03T17:42:13Z")
Hello, I am trying to write a script to automate the cropping of volume for quite a few CT scans using Python. Thanks to the previous questions and the documentation, I have been able to figure out pretty much the whole… --- ## [Cropped volume is not accessible](https://discourse.slicer.org/t/cropped-volume-is-not-accessible/17732)
**Author:** [@KAVIYA\_DHARSHINI](https://discourse.slicer.org/u/KAVIYA_DHARSHINI)\ **Replies:** 1\ **Last updated:** [May 23, 2021, 7:02pm UTC](https://discourse.slicer.org/t/cropped-volume-is-not-accessible/17732 "2021-05-23T19:02:34Z")
Operating system:windows 10 ,64bit Slicer version:4.1120200930 Expected behavior: able to load and do other operations with cropped volume . Actual behavior: I want to run python script to load an dicom series, get ro… --- ## [Post-crop return to original volume and re-crop](https://discourse.slicer.org/t/post-crop-return-to-original-volume-and-re-crop/11677)
**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\ **Replies:** 1\ **Last updated:** [May 23, 2020, 6:29pm UTC](https://discourse.slicer.org/t/post-crop-return-to-original-volume-and-re-crop/11677 "2020-05-23T18:29:34Z")
Operating system:windows 10 Slicer version: enter dicom successfully crop and segment is there any way to return to the original volume to do another crop? thx --- ## [Change of the sign of space directions and space origin due to interpolation / cropping](https://discourse.slicer.org/t/change-of-the-sign-of-space-directions-and-space-origin-due-to-interpolation-cropping/10864)
**Author:** [@MMMPPPMMM](https://discourse.slicer.org/u/MMMPPPMMM)\ **Replies:** 1\ **Last updated:** [March 26, 2020, 11:14pm UTC](https://discourse.slicer.org/t/change-of-the-sign-of-space-directions-and-space-origin-due-to-interpolation-cropping/10864 "2020-03-26T23:14:03Z")
Hello Is it intended that the sign of space directions and space origin change due to interpolated cropping? From the header files of the volumes: Before interpolation / cropping: type: float dimension: 3 space: l…