# \#roi **URL:** https://discourse.slicer.org/tag/roi/444.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [Transformed ROI shows up as changed in Save dialog directly after opening an mrml scene](https://discourse.slicer.org/t/transformed-roi-shows-up-as-changed-in-save-dialog-directly-after-opening-an-mrml-scene/43384)
**Author:** [@MMMPPPMMM](https://discourse.slicer.org/u/MMMPPPMMM)\ **Replies:** 3\ **Last updated:** [July 27, 2025, 10:13am UTC](https://discourse.slicer.org/t/transformed-roi-shows-up-as-changed-in-save-dialog-directly-after-opening-an-mrml-scene/43384 "2025-07-27T10:13:41Z")
Hello I think it is a bug that a transformed ROI shows up as changed in Save dialog directly after opening an MRML scene? Find an example here: Download Transformed\_ROI\_Test.zip | LimeWire Tested with Slicer 5.8.1 … --- ## [ROI of 3 stl files](https://discourse.slicer.org/t/roi-of-3-stl-files/43722)
**Author:** [@PLET](https://discourse.slicer.org/u/PLET)\ **Replies:** 3\ **Last updated:** [July 15, 2025, 2:55pm UTC](https://discourse.slicer.org/t/roi-of-3-stl-files/43722 "2025-07-15T14:55:41Z")
I have 3 .stl files of a forearm segment (muscle, skin, bone). I want to use 3D Slicer to crop a specific section, but I can only do it with one layer. I don’t know how to crop all three layers together at the same time.… --- ## [Is it possible in pyradiomics to normalize only the ROI and not the entire image?](https://discourse.slicer.org/t/is-it-possible-in-pyradiomics-to-normalize-only-the-roi-and-not-the-entire-image/43721)
**Author:** [@Alessandro\_Ghilardi](https://discourse.slicer.org/u/Alessandro_Ghilardi)\ **Replies:** 0\ **Last updated:** [July 15, 2025, 4:26am UTC](https://discourse.slicer.org/t/is-it-possible-in-pyradiomics-to-normalize-only-the-roi-and-not-the-entire-image/43721 "2025-07-15T04:26:26Z")
I need to know if there’s a standard way to normalize only the ROI. I tried to create a function to do so but in this case filtered versions of the image would be calculated only after the ROI normalization (which means … --- ## [Creating a boundary box after rotating/translating a volume](https://discourse.slicer.org/t/creating-a-boundary-box-after-rotating-translating-a-volume/42343)
**Author:** [@coco](https://discourse.slicer.org/u/coco)\ **Replies:** 4\ **Last updated:** [April 2, 2025, 9:30am UTC](https://discourse.slicer.org/t/creating-a-boundary-box-after-rotating-translating-a-volume/42343 "2025-04-02T09:30:12Z")
Dear all, I’m having some issues creating a bounding box arround my segment after registering a volume and segments. As you can see on the picture, the calculated bounding box “sticks” to the original volume geometry b… --- ## [Volume compressed into ROI](https://discourse.slicer.org/t/volume-compressed-into-roi/40085)
**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")
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 … --- ## [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… --- ## [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… --- ## [Extract/Save ROI from seg.nrrd (segmentations file) using Python packages SimpleITK or Slicerio](https://discourse.slicer.org/t/extract-save-roi-from-seg-nrrd-segmentations-file-using-python-packages-simpleitk-or-slicerio/33374)
**Author:** [@Vishal\_P](https://discourse.slicer.org/u/Vishal_P)\ **Replies:** 4\ **Last updated:** [December 27, 2023, 11:44pm UTC](https://discourse.slicer.org/t/extract-save-roi-from-seg-nrrd-segmentations-file-using-python-packages-simpleitk-or-slicerio/33374 "2023-12-27T23:44:51Z")
Hello! I have a .nii scan file and have successfully created segments, saving them in a .seg.nrrd file. My goal now is to extract ROIs based on label names and save them as new .nii files. To achieve this, I am explorin… --- ## [Gray Level Co-occurrence Matrix](https://discourse.slicer.org/t/gray-level-co-occurrence-matrix/32673)
**Author:** [@foursheep](https://discourse.slicer.org/u/foursheep)\ **Replies:** 0\ **Last updated:** [November 8, 2023, 2:09pm UTC](https://discourse.slicer.org/t/gray-level-co-occurrence-matrix/32673 "2023-11-08T14:09:04Z")
Hi, I am preparing to extract the features of the outer circular region of the ROI. Can I directly input the circular ROI to obtain GLCM Features? --- ## [Save and import ROI for multiple MRI series](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30822)
**Author:** [@EduardVerheijen](https://discourse.slicer.org/u/EduardVerheijen)\ **Replies:** 0\ **Last updated:** [July 27, 2023, 12:19am UTC](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30822 "2023-07-27T00:19:45Z")
Hi all, I am new to using 3D slicer. For a project I want to crop a 400x400 pixel ROI box from axial MRI scans and export them as DICOM. I managed to do it for one patient’s MRI series, but I need to have the exact same… --- ## [Save and import ROI for multiple MRI series](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30814)
**Author:** [@EduardVerheijen](https://discourse.slicer.org/u/EduardVerheijen)\ **Replies:** 0\ **Last updated:** [July 26, 2023, 8:16pm UTC](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30814 "2023-07-26T20:16:42Z")
Hi all, I am new to using 3D slicer. For a project I want to crop a 400x400 pixel ROI box from axial MRI scans and export them as DICOM. I managed to do it for one patient’s MRI series, but I need to have the exact same… --- ## [Use MarkupsROI to crop DICOM in coronal / sagittal view](https://discourse.slicer.org/t/use-markupsroi-to-crop-dicom-in-coronal-sagittal-view/30399)
**Author:** [@dhanushkannan](https://discourse.slicer.org/u/dhanushkannan)\ **Replies:** 0\ **Last updated:** [July 5, 2023, 3:28am UTC](https://discourse.slicer.org/t/use-markupsroi-to-crop-dicom-in-coronal-sagittal-view/30399 "2023-07-05T03:28:41Z")
Hi all, I have used MarkupsROI to crop DICOM images using Python. the following is the code which I have used for cropping based on ROI cropVolumeLogic = slicer.modules.cropvolume.logic() cropVolumeParameterNode = … --- ## [Creat a circular ROI and extract count in PET image](https://discourse.slicer.org/t/creat-a-circular-roi-and-extract-count-in-pet-image/28501)
**Author:** [@Shearson](https://discourse.slicer.org/u/Shearson)\ **Replies:** 2\ **Last updated:** [March 21, 2023, 8:17pm UTC](https://discourse.slicer.org/t/creat-a-circular-roi-and-extract-count-in-pet-image/28501 "2023-03-21T20:17:28Z")
Dear members, I have a series of PET images of the same phantom. Now I’m trying to create a fixed size (like diameter=10mm) circular ROI in the same position of each series and extract the count or SUV. Is it possible or… --- ## [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… --- ## [Fiducial markers hidden when cropping ROI disabled, and shown when cropping ROI enabled](https://discourse.slicer.org/t/fiducial-markers-hidden-when-cropping-roi-disabled-and-shown-when-cropping-roi-enabled/22665)
**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\ **Replies:** 3\ **Last updated:** [March 24, 2022, 1:20pm UTC](https://discourse.slicer.org/t/fiducial-markers-hidden-when-cropping-roi-disabled-and-shown-when-cropping-roi-enabled/22665 "2022-03-24T13:20:38Z")
I created a fiducial maker that was located just outside a cropping ROI. When cropping ROI is enabled and displayed, the external fiducial marker isn’t shown (this is logical). When cropping ROI is enabled but not disp…