# Support **URL:** https://discourse.slicer.org/c/support/11.md?page=343 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 344 --- ## [Problem uploading MRI image](https://discourse.slicer.org/t/problem-uploading-mri-image/11269)
**Author:** [@youssef](https://discourse.slicer.org/u/youssef)\ **Replies:** 9\ **Last updated:** [April 25, 2020, 4:43pm UTC](https://discourse.slicer.org/t/problem-uploading-mri-image/11269 "2020-04-25T16:43:21Z")
Operating system: WINDOWS 10 Slicer version: 4.10.2 I have a problem when I load the file (MRI DICOM) as you see below I used the DICOM module and I followed tips in the DICOM FAQ, but i have the same problem. --- ## [Creating .mha files ](https://discourse.slicer.org/t/creating-mha-files/6557)
**Author:** [@xaris\_komninos](https://discourse.slicer.org/u/xaris_komninos)\ **Replies:** 52\ **Last updated:** [April 25, 2020, 1:37pm UTC](https://discourse.slicer.org/t/creating-mha-files/6557 "2020-04-25T13:37:54Z")
Hi, I want to reconstruct the volume of a kidney, in real time, using a sequence of 2D Ultrasound images. The 2D images are obtained by a probe and the position of the probe is given by the kinematics of the da vinci r… --- ## [Is there interest in higher quality rendering for Slicer?](https://discourse.slicer.org/t/is-there-interest-in-higher-quality-rendering-for-slicer/6862)
**Author:** [@Dave\_DeMarle](https://discourse.slicer.org/u/Dave_DeMarle)\ **Replies:** 6\ **Last updated:** [April 25, 2020, 6:30am UTC](https://discourse.slicer.org/t/is-there-interest-in-higher-quality-rendering-for-slicer/6862 "2020-04-25T06:30:15Z")
Hello, If I may, I would like to ask the group if there is significant interest in future extensions to Slicer that would bridge the gap to photorealistic rendering? In the ParaView world we’ve been doing work with NVi… --- ## [Coloring surfaces in slicer](https://discourse.slicer.org/t/coloring-surfaces-in-slicer/11202)
**Author:** [@hcmidt](https://discourse.slicer.org/u/hcmidt)\ **Replies:** 20\ **Last updated:** [April 25, 2020, 3:02am UTC](https://discourse.slicer.org/t/coloring-surfaces-in-slicer/11202 "2020-04-25T03:02:13Z")
Hello together, I have written a couple of python scripts to analyze CT scan images and would like to depict the results in slicer. My script returns a 3d array that assigns a thickness to each point on a surface (let’… --- ## [How can I import NIFTI files to DSCMRIAnalysis module?](https://discourse.slicer.org/t/how-can-i-import-nifti-files-to-dscmrianalysis-module/3645)
**Author:** [@Kyu\_Sung\_Choi](https://discourse.slicer.org/u/Kyu_Sung_Choi)\ **Replies:** 11\ **Last updated:** [April 24, 2020, 11:18pm UTC](https://discourse.slicer.org/t/how-can-i-import-nifti-files-to-dscmrianalysis-module/3645 "2020-04-24T23:18:55Z")
Dear Dr. Fedorov, I’ve decided to correct motion of 4D DSC dicom files. However, after motion correction, the 4D DSC dicom files should be in NIFTI format. So I saved the NIFTI output file into NRRD file using slicer… --- ## [How to split one segment into three equal parts via script?](https://discourse.slicer.org/t/how-to-split-one-segment-into-three-equal-parts-via-script/11287)
**Author:** [@Ezio\_Lanza](https://discourse.slicer.org/u/Ezio_Lanza)\ **Replies:** 1\ **Last updated:** [April 24, 2020, 4:05pm UTC](https://discourse.slicer.org/t/how-to-split-one-segment-into-three-equal-parts-via-script/11287 "2020-04-24T16:05:19Z")
Hi, I need to create a script that splits one segment (e.g. volume lung) into three equal parts to simulate the three different lung lobes. (upper, mid and lower part). Is there a good example to start or can you provi… --- ## [How to change segmentID of existing segmentations](https://discourse.slicer.org/t/how-to-change-segmentid-of-existing-segmentations/11254)
**Author:** [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\ **Replies:** 6\ **Last updated:** [April 24, 2020, 2:27pm UTC](https://discourse.slicer.org/t/how-to-change-segmentid-of-existing-segmentations/11254 "2020-04-24T14:27:32Z")
Hi all, How can I change the segmentIDs/tags of existing segmentations? Currently, saving a colour table results in these default values (in bold) but I would like to set my own tags for the existing segmentations that … --- ## [Is it possible to extract used threshold from segment editor?](https://discourse.slicer.org/t/is-it-possible-to-extract-used-threshold-from-segment-editor/11289)
**Author:** [@ASR225](https://discourse.slicer.org/u/ASR225)\ **Replies:** 0\ **Last updated:** [April 24, 2020, 1:05pm UTC](https://discourse.slicer.org/t/is-it-possible-to-extract-used-threshold-from-segment-editor/11289 "2020-04-24T13:05:36Z")
Hi, I have a simple question. I could not find the answer that’s why I made a new topic. So I use 3d Slicer to calculate volumes with segment editor. first, I create a new segment and I use a threshold to select the p… --- ## [how to crop a image using a mask](https://discourse.slicer.org/t/how-to-crop-a-image-using-a-mask/11288)
**Author:** [@zhou\_zhou](https://discourse.slicer.org/u/zhou_zhou)\ **Replies:** 0\ **Last updated:** [April 24, 2020, 1:05pm UTC](https://discourse.slicer.org/t/how-to-crop-a-image-using-a-mask/11288 "2020-04-24T13:05:30Z")
Hi dear all, Do you know how to crop the T1 brain image using a mask? best zhou --- ## [Voxel-based finite element modeling](https://discourse.slicer.org/t/voxel-based-finite-element-modeling/11223)
**Author:** [@Vasyl](https://discourse.slicer.org/u/Vasyl)\ **Replies:** 6\ **Last updated:** [April 24, 2020, 12:32am UTC](https://discourse.slicer.org/t/voxel-based-finite-element-modeling/11223 "2020-04-24T00:32:19Z")
Hy everybody! I’m only a beginner in segmentation and meshing models and I have one precise question: how can I create voxel-based FE model. I’ve already read some articles dedicated to this topic (GitHub - lassoan/Sli… --- ## [Liver tumor segmentation from ultrasound 3D (GE Voluson machine)](https://discourse.slicer.org/t/liver-tumor-segmentation-from-ultrasound-3d-ge-voluson-machine/11272)
**Author:** [@emipaw](https://discourse.slicer.org/u/emipaw)\ **Replies:** 1\ **Last updated:** [April 23, 2020, 6:55pm UTC](https://discourse.slicer.org/t/liver-tumor-segmentation-from-ultrasound-3d-ge-voluson-machine/11272 "2020-04-23T18:55:06Z")
Hi, I am new in Slicer 3D. I want to segment a liver tumor from ultrasound 3D examine in .vol format. I tried to do it using Volume Rendering but the 3D model doesn’tt look good. I tried to choose every preset and ther… --- ## [Is there a way to integrate 3D slicer and ROS?](https://discourse.slicer.org/t/is-there-a-way-to-integrate-3d-slicer-and-ros/11266)
**Author:** [@CHRIS\_HUYNH](https://discourse.slicer.org/u/CHRIS_HUYNH)\ **Replies:** 1\ **Last updated:** [April 23, 2020, 1:22pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-integrate-3d-slicer-and-ros/11266 "2020-04-23T13:22:38Z")
Hi, I’m using the pedicle screw simulator to plan pedicle screw trajectories and I was wondering if i was able to use these planned trajectories in 3D Slicer to position an ABB 120 robot to align with these trajectories… --- ## [Help over VisSimTools](https://discourse.slicer.org/t/help-over-vissimtools/8203)
**Author:** [@Baez](https://discourse.slicer.org/u/Baez)\ **Replies:** 4\ **Last updated:** [April 23, 2020, 9:27am UTC](https://discourse.slicer.org/t/help-over-vissimtools/8203 "2020-04-23T09:27:20Z")
Hi community. I have a question, I try to segment the cervical spine with the VisSimTools / Cervical Spine Tools module. It works well with the Bc11702 data set of the DataStore module. But wanting to do it with studi… --- ## [ID threshold upper and lower limits from saved scene](https://discourse.slicer.org/t/id-threshold-upper-and-lower-limits-from-saved-scene/11258)
**Author:** [@mccarthyvetsurg](https://discourse.slicer.org/u/mccarthyvetsurg)\ **Replies:** 1\ **Last updated:** [April 23, 2020, 6:14am UTC](https://discourse.slicer.org/t/id-threshold-upper-and-lower-limits-from-saved-scene/11258 "2020-04-23T06:14:06Z")
Is there anyway to identify threshold limits from a saved scene of an STL for example. I can upload the volume and it has the threshold outlined, but am not able to see the threshold limits used to make the STL. Thanks… --- ## [Loading MRB file breaks linked views](https://discourse.slicer.org/t/loading-mrb-file-breaks-linked-views/5951)
**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\ **Replies:** 2\ **Last updated:** [April 22, 2020, 8:25pm UTC](https://discourse.slicer.org/t/loading-mrb-file-breaks-linked-views/5951 "2020-04-22T20:25:09Z")
This issue can be replicated using by the following steps: load MRIHead and render in Dual 3D save as an MRB file reopen Slicer, load MRB file use link/unlink buttons in 3D view windows to link views The viewers canno… --- ## [Extracting a 2d oblique plane using itk/vtk via python, (as shown in slicer view)](https://discourse.slicer.org/t/extracting-a-2d-oblique-plane-using-itk-vtk-via-python-as-shown-in-slicer-view/11250)
**Author:** [@helenawill95](https://discourse.slicer.org/u/helenawill95)\ **Replies:** 5\ **Last updated:** [April 22, 2020, 8:19pm UTC](https://discourse.slicer.org/t/extracting-a-2d-oblique-plane-using-itk-vtk-via-python-as-shown-in-slicer-view/11250 "2020-04-22T20:19:43Z")
Hello, I am currently using Slicer to manually find a slice- but I need to automate this. I was wondering if you could share any information how slicer displays the coronal view. My volume has a direction matrix \[0.9713… --- ## [Enhancing Orbital Walls With Unsharp Mask Filtering](https://discourse.slicer.org/t/enhancing-orbital-walls-with-unsharp-mask-filtering/8440)
**Author:** [@Juicy](https://discourse.slicer.org/u/Juicy)\ **Replies:** 9\ **Last updated:** [April 22, 2020, 7:47pm UTC](https://discourse.slicer.org/t/enhancing-orbital-walls-with-unsharp-mask-filtering/8440 "2020-04-22T19:47:01Z")
Hello all, I was looking into ways to make segmenting eye orbits a bit easier (for bio models in the public hospital) I found this handy list of hints segmentation of thin surfaces I have also read through the masters… --- ## [Batch segment creation - macro](https://discourse.slicer.org/t/batch-segment-creation-macro/11123)
**Author:** [@Ezio\_Lanza](https://discourse.slicer.org/u/Ezio_Lanza)\ **Replies:** 4\ **Last updated:** [April 22, 2020, 6:31pm UTC](https://discourse.slicer.org/t/batch-segment-creation-macro/11123 "2020-04-22T18:31:23Z")
Dear all, Is there a way to instruct segment editor to do the following operations with one click ? Let me offer an example: I have the segment LUNG which comprises the whole lung volume. I would like with one click t… --- ## [Volume rendering produces block of "white noise"](https://discourse.slicer.org/t/volume-rendering-produces-block-of-white-noise/10572)
**Author:** [@Mark\_1](https://discourse.slicer.org/u/Mark_1)\ **Replies:** 38\ **Last updated:** [April 22, 2020, 12:12pm UTC](https://discourse.slicer.org/t/volume-rendering-produces-block-of-white-noise/10572 "2020-04-22T12:12:36Z")
Hello, I’m very new to using 3D Slicer (this is my first day) so apologies if this is a very basic issue, but I’ve been trying to produce a volume render of a microCT scan of a skull and all that I get is a block of whi… --- ## [Using 3DSlicer for Optical Coherence Tomography (St Jude's)](https://discourse.slicer.org/t/using-3dslicer-for-optical-coherence-tomography-st-judes/494)
**Author:** [@Jaytee](https://discourse.slicer.org/u/Jaytee)\ **Replies:** 10\ **Last updated:** [April 22, 2020, 3:19pm UTC](https://discourse.slicer.org/t/using-3dslicer-for-optical-coherence-tomography-st-judes/494 "2020-04-22T15:19:04Z")
Hi Everyone, I’m very new to 3D slicer, I just downloaded it to try get some 3D images for a case report but having some trouble. Not sure if anyone has experience in using the St Jude’s OCT system (used in cardiology … --- ## [load dicom images generated by dcmtk ](https://discourse.slicer.org/t/load-dicom-images-generated-by-dcmtk/11247)
**Author:** [@filipaferreira](https://discourse.slicer.org/u/filipaferreira)\ **Replies:** 3\ **Last updated:** [April 22, 2020, 2:56pm UTC](https://discourse.slicer.org/t/load-dicom-images-generated-by-dcmtk/11247 "2020-04-22T14:56:06Z")
Hi, I’m using dcmtk to load dicom images using cmd. But when I load the image it comes very grayish and opaque, we can´t see anything. And the original image shows an abdomen. Any Idea what could be? (I’m using a tcp… --- ## [Can slicer be used to segment radially orientated DICOM images?](https://discourse.slicer.org/t/can-slicer-be-used-to-segment-radially-orientated-dicom-images/11246)
**Author:** [@Jiang\_Yao](https://discourse.slicer.org/u/Jiang_Yao)\ **Replies:** 1\ **Last updated:** [April 22, 2020, 1:20pm UTC](https://discourse.slicer.org/t/can-slicer-be-used-to-segment-radially-orientated-dicom-images/11246 "2020-04-22T13:20:24Z")
Operating system: windows 10 Slicer version: 4.10.2 r28257 Expected behavior: I have a set of dicom images that are rotating radially with 10 degrees apart, totally 18 slices for left ventricle in the heart. Actual b… --- ## [Question about batchstructureset conversion](https://discourse.slicer.org/t/question-about-batchstructureset-conversion/11235)
**Author:** [@codecrazer](https://discourse.slicer.org/u/codecrazer)\ **Replies:** 4\ **Last updated:** [April 22, 2020, 12:41pm UTC](https://discourse.slicer.org/t/question-about-batchstructureset-conversion/11235 "2020-04-22T12:41:21Z")
Dear colleague, I have used the batchstructuresetconversion script, it is very convenience. However, the output file or NRRD didn’t contain the origin patinet ID, how could I do it? Thanks for your help! --- ## [Wrap Solidify segment editor effect for filling smaller holes](https://discourse.slicer.org/t/wrap-solidify-segment-editor-effect-for-filling-smaller-holes/11242)
**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\ **Replies:** 0\ **Last updated:** [April 22, 2020, 10:25am UTC](https://discourse.slicer.org/t/wrap-solidify-segment-editor-effect-for-filling-smaller-holes/11242 "2020-04-22T10:25:57Z")
I just saw the youtube video about the Wrap Solidify effect, very nice work! I’d like to ask about its potential usage to fill smaller holes. Looking at this screenshot, I can see that there is a Custom region mode, whi… --- ## [Fail to Run Slicer.sln in debug mode](https://discourse.slicer.org/t/fail-to-run-slicer-sln-in-debug-mode/11224)
**Author:** [@kobidk](https://discourse.slicer.org/u/kobidk)\ **Replies:** 3\ **Last updated:** [April 22, 2020, 8:56am UTC](https://discourse.slicer.org/t/fail-to-run-slicer-sln-in-debug-mode/11224 "2020-04-22T08:56:02Z")
Operating system:Windows 10 Slicer version:4.10. Expected behavior: Loading the Slicer App using Slicer.slh in debug mode Actual behavior: Fails to load some Dlls files integrated into the Slicer project. I’m trying … --- ## [Cannot load/import Dicom data](https://discourse.slicer.org/t/cannot-load-import-dicom-data/11215)
**Author:** [@tnmd33](https://discourse.slicer.org/u/tnmd33)\ **Replies:** 2\ **Last updated:** [April 21, 2020, 6:21pm UTC](https://discourse.slicer.org/t/cannot-load-import-dicom-data/11215 "2020-04-21T18:21:55Z")
Problem report for Slicer 4.10.2 win-amd64: Hi, I’m new to 3D slicer, I wanted to import DICOM data from a CT but got this error that I don’t understand, this is from the log file: \[DEBUG\]\[Qt\] 20.04.2020 20:40:06 \[\] (un… --- ## [File export / saving trouble ](https://discourse.slicer.org/t/file-export-saving-trouble/11184)
**Author:** [@Allison\_Brea](https://discourse.slicer.org/u/Allison_Brea)\ **Replies:** 11\ **Last updated:** [April 21, 2020, 12:27am UTC](https://discourse.slicer.org/t/file-export-saving-trouble/11184 "2020-04-21T00:27:53Z")
Hi all, I have an annotated CT scan data set that I am having trouble saving on my Mac Book Pro laptop. I have tried to save the set several times changing the file format and saving it in many places on the computer bu… --- ## [Error when importing cv2.aruco in python file](https://discourse.slicer.org/t/error-when-importing-cv2-aruco-in-python-file/11176)
**Author:** [@cyrillajarge](https://discourse.slicer.org/u/cyrillajarge)\ **Replies:** 2\ **Last updated:** [April 20, 2020, 6:44pm UTC](https://discourse.slicer.org/t/error-when-importing-cv2-aruco-in-python-file/11176 "2020-04-20T18:44:00Z")
Hi guys, I’m developing a module for a school project in which I need to use OpenCV combined with Aruco. I have installed the extension SlicerOpenCV and OpenCV is working correctly when I import cv2 in my python file. … --- ## [Radiomics problem for VUE images](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207)
**Author:** [@aileeno](https://discourse.slicer.org/u/aileeno)\ **Replies:** 4\ **Last updated:** [April 20, 2020, 6:28pm UTC](https://discourse.slicer.org/t/radiomics-problem-for-vue-images/11207 "2020-04-20T18:28:54Z")
Operating system: macOS Catalina Slicer version: 4.10.2 Expected behavior: extract radiomics features from a label map created from a virtual unenhanced CT (dual energy) Actual behavior: No features extracted, followi… --- ## [Mouse PET/CT to MRI registration error](https://discourse.slicer.org/t/mouse-pet-ct-to-mri-registration-error/11016)
**Author:** [@Kate\_Day](https://discourse.slicer.org/u/Kate_Day)\ **Replies:** 5\ **Last updated:** [April 20, 2020, 4:23pm UTC](https://discourse.slicer.org/t/mouse-pet-ct-to-mri-registration-error/11016 "2020-04-20T16:23:37Z")
I’m new to Slicer. I need to register an MRI with a PET/CT. The PET and CT register easily though they were taken by the same equipment at the same time. When I attempt to register the MRI with the CT it gives me an erro… [Previous page](https://discourse.slicer.org/c/support/11.md?page=342) [Next page](https://discourse.slicer.org/c/support/11.md?page=344)