# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=129

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

**Page:** 130

---

## [ALPACA module doesn't correctly register models of different size](https://discourse.slicer.org/t/alpaca-module-doesnt-correctly-register-models-of-different-size/13208)

<div class="topic-metadata">

**Author:** [@Dave\_Matthews](https://discourse.slicer.org/u/Dave_Matthews)\
**Replies:** 6\
**Last updated:** [November 16, 2023, 3:50pm UTC](https://discourse.slicer.org/t/alpaca-module-doesnt-correctly-register-models-of-different-size/13208 "2023-11-16T15:50:45Z")

</div>

I’ve segmented out the premaxilla of several guppies that I CT scanned. I place landmarks on one of the models and am trying to use ALPACA to transfer these landmarks to other models. This works well when I use two model…

---

## [Material mapping for bone from CT scan](https://discourse.slicer.org/t/material-mapping-for-bone-from-ct-scan/32837)

<div class="topic-metadata">

**Author:** [@ElaniaDiBart](https://discourse.slicer.org/u/ElaniaDiBart)\
**Replies:** 3\
**Last updated:** [November 16, 2023, 2:59pm UTC](https://discourse.slicer.org/t/material-mapping-for-bone-from-ct-scan/32837 "2023-11-16T14:59:50Z")

</div>

Hi all, I’m attempting material mapping for mechanical properties in bones. I’ve previously achieved this in MITK-Gen by correlating Hounsfield Units (HS units) with bone density, followed by computing the elastic modul…

---

## [Is there a way to have all vertices on a vtk model be markups/landmarks?](https://discourse.slicer.org/t/is-there-a-way-to-have-all-vertices-on-a-vtk-model-be-markups-landmarks/28752)

<div class="topic-metadata">

**Author:** [@Gening\_Dong](https://discourse.slicer.org/u/Gening_Dong)\
**Replies:** 4\
**Last updated:** [November 16, 2023, 8:52am UTC](https://discourse.slicer.org/t/is-there-a-way-to-have-all-vertices-on-a-vtk-model-be-markups-landmarks/28752 "2023-11-16T08:52:55Z")

</div>

Hi, I’m trying to match the node IDs between two vtk models. I was thinking if it’s possible to have all vertices on a vtk model be markups, so that I can directly use the vertices on the surface of the source model as …

---

## [Intensity Segmenter; Range file](https://discourse.slicer.org/t/intensity-segmenter-range-file/32852)

<div class="topic-metadata">

**Author:** [@bushra](https://discourse.slicer.org/u/bushra)\
**Replies:** 0\
**Last updated:** [November 16, 2023, 3:10am UTC](https://discourse.slicer.org/t/intensity-segmenter-range-file/32852 "2023-11-16T03:10:48Z")

</div>

Hello, How to prepare intensity range file? I need step by step guidance for this.

---

## [Finding center of designated points](https://discourse.slicer.org/t/finding-center-of-designated-points/32841)

<div class="topic-metadata">

**Author:** [@lccmyers](https://discourse.slicer.org/u/lccmyers)\
**Replies:** 1\
**Last updated:** [November 16, 2023, 12:42am UTC](https://discourse.slicer.org/t/finding-center-of-designated-points/32841 "2023-11-16T00:42:50Z")

</div>

I’m trying to figure out how to find the center of 4+ points that I place on a 3D model. I’m placing the points on two separate models (they’re vertebrae) and the center point would lie in the space in between the models…

---

## [Intensity Segmenter - Range file](https://discourse.slicer.org/t/intensity-segmenter-range-file/25478)

<div class="topic-metadata">

**Author:** [@hortakc](https://discourse.slicer.org/u/hortakc)\
**Replies:** 2\
**Last updated:** [November 16, 2023, 12:37am UTC](https://discourse.slicer.org/t/intensity-segmenter-range-file/25478 "2023-11-16T00:37:40Z")

</div>

Hello, I am trying to apply the Range file ( .txt file) in the Intensity Segmenter module, but it is not charging or segmenting. I used this range file when using the Slicer 4.0, now, I only have the newest version 5.0. …

---

## [Mitral valve segmentation from Ge TEE Dicom](https://discourse.slicer.org/t/mitral-valve-segmentation-from-ge-tee-dicom/32843)

<div class="topic-metadata">

**Author:** [@KatellD](https://discourse.slicer.org/u/KatellD)\
**Replies:** 2\
**Last updated:** [November 15, 2023, 9:33pm UTC](https://discourse.slicer.org/t/mitral-valve-segmentation-from-ge-tee-dicom/32843 "2023-11-15T21:33:00Z")

</div>

Hi all, I am trying to segment a mitral valve from 3D TEE for reseach purposes and the software seems to not recognize the different axis (axial, sagittal, coronal). After multiple attempts to restore the Dicom fram…

---

## [Large data set, not enough memory, Slicer crashes](https://discourse.slicer.org/t/large-data-set-not-enough-memory-slicer-crashes/32783)

<div class="topic-metadata">

**Author:** [@Susan\_Marriott](https://discourse.slicer.org/u/Susan_Marriott)\
**Replies:** 5\
**Last updated:** [November 15, 2023, 5:20pm UTC](https://discourse.slicer.org/t/large-data-set-not-enough-memory-slicer-crashes/32783 "2023-11-15T17:20:16Z")

</div>

Operating system: MacOS Slicer version: Expected behavior: Actual behavior: crashes I have data sets of 3000+ images derived from CT scans of rocks containing trace fossils. I am trying to find out what the architec…

---

## [Cannot download extension file](https://discourse.slicer.org/t/cannot-download-extension-file/32797)

<div class="topic-metadata">

**Author:** [@park](https://discourse.slicer.org/u/park)\
**Replies:** 3\
**Last updated:** [November 15, 2023, 3:43pm UTC](https://discourse.slicer.org/t/cannot-download-extension-file/32797 "2023-11-15T15:43:59Z")

</div>

Hi all, I am currently unable to download extension files from the Slicer server these days, although it worked well before. The error message is: “Failed downloading: https://slicer-packages.kitware.com/api/v1/file” …

---

## [How to export a picture of the desired size](https://discourse.slicer.org/t/how-to-export-a-picture-of-the-desired-size/32836)

<div class="topic-metadata">

**Author:** [@bancheng33](https://discourse.slicer.org/u/bancheng33)\
**Replies:** 0\
**Last updated:** [November 15, 2023, 12:26pm UTC](https://discourse.slicer.org/t/how-to-export-a-picture-of-the-desired-size/32836 "2023-11-15T12:26:15Z")

</div>

Dear Sir! The size of the image I exported is similar to the scale in the image. But I want to export a picture of the scale of the figure in the image below. Could you please tell me the specific procedure? Tha…

---

## [Convert between MultiVolume and Volume Sequence?](https://discourse.slicer.org/t/convert-between-multivolume-and-volume-sequence/24504)

<div class="topic-metadata">

**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 21\
**Last updated:** [November 15, 2023, 6:15am UTC](https://discourse.slicer.org/t/convert-between-multivolume-and-volume-sequence/24504 "2023-11-15T06:15:03Z")

</div>

Hello, I am interested in doing perfusion analysis on dynamic contrast enhanced MRI images using Slicer. I see that there are two older extensions which allow this, PkModeling and DSCMRIAnalysis, both of which are CLI m…

---

## [Material mapping for bones](https://discourse.slicer.org/t/material-mapping-for-bones/32828)

<div class="topic-metadata">

**Author:** [@ElaniaDiBart](https://discourse.slicer.org/u/ElaniaDiBart)\
**Replies:** 0\
**Last updated:** [November 15, 2023, 5:46am UTC](https://discourse.slicer.org/t/material-mapping-for-bones/32828 "2023-11-15T05:46:18Z")

</div>

Hi all, I’m attempting material mapping for mechanical properties in bones. I’ve previously achieved this in MITK-Gem by correlating Hounsfield Units (HU units) with bone density, followed by computing the elastic modul…

---

## [Integration of Fast Growcut extension for 3D slicer](https://discourse.slicer.org/t/integration-of-fast-growcut-extension-for-3d-slicer/32786)

<div class="topic-metadata">

**Author:** [@Shreyas\_reddy](https://discourse.slicer.org/u/Shreyas_reddy)\
**Replies:** 2\
**Last updated:** [November 14, 2023, 11:20pm UTC](https://discourse.slicer.org/t/integration-of-fast-growcut-extension-for-3d-slicer/32786 "2023-11-14T23:20:29Z")

</div>

Hi everybody, Subject: Inquiry on Integrating Fast GrowCut Software with Latest 3D Slicer Version Dear 3D Slicer Developer Community, I am currently working on a project that involves utilizing Fast GrowCut software f…

---

## [Keep lung from different subjects has the same number of nodes/ landmarks](https://discourse.slicer.org/t/keep-lung-from-different-subjects-has-the-same-number-of-nodes-landmarks/32814)

<div class="topic-metadata">

**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 0\
**Last updated:** [November 14, 2023, 5:29pm UTC](https://discourse.slicer.org/t/keep-lung-from-different-subjects-has-the-same-number-of-nodes-landmarks/32814 "2023-11-14T17:29:18Z")

</div>

Hi, I need to do the segmentation for lung in different subjects. And then I need to conduct principal component analysis (PCA). Because usually PCA needs the landmarks information, and every subject must have the same…

---

## [How can i use 3DSlicer in a not local host container to do a brain segmentation of a Photon-Counting CT (totalsegmentor extension)?](https://discourse.slicer.org/t/how-can-i-use-3dslicer-in-a-not-local-host-container-to-do-a-brain-segmentation-of-a-photon-counting-ct-totalsegmentor-extension/32785)

<div class="topic-metadata">

**Author:** [@Carolina\_Alves](https://discourse.slicer.org/u/Carolina_Alves)\
**Replies:** 3\
**Last updated:** [November 14, 2023, 1:30pm UTC](https://discourse.slicer.org/t/how-can-i-use-3dslicer-in-a-not-local-host-container-to-do-a-brain-segmentation-of-a-photon-counting-ct-totalsegmentor-extension/32785 "2023-11-14T13:30:59Z")

</div>

I do not know how to install the 3DSlicer in my not localhost container xc. I pretend to use the total segmentor extension in a jupyter notebook of my container. This is for my master thesis about segmentation a PCCT.

---

## [Apply Transforms in only 1 segment](https://discourse.slicer.org/t/apply-transforms-in-only-1-segment/32804)

<div class="topic-metadata">

**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 1\
**Last updated:** [November 14, 2023, 1:23pm UTC](https://discourse.slicer.org/t/apply-transforms-in-only-1-segment/32804 "2023-11-14T13:23:22Z")

</div>

Hi to everyone :slight\_smile: In this case I’m struggling with transformations and Segmentations. The problem is the following one: -I’m trying to apply by code a linear transformation to a specific segment contained i…

---

## [Tumour Segmentation enquiry](https://discourse.slicer.org/t/tumour-segmentation-enquiry/32799)

<div class="topic-metadata">

**Author:** [@Sefa\_Waqarua](https://discourse.slicer.org/u/Sefa_Waqarua)\
**Replies:** 3\
**Last updated:** [November 14, 2023, 4:32am UTC](https://discourse.slicer.org/t/tumour-segmentation-enquiry/32799 "2023-11-14T04:32:38Z")

</div>

Hello I’m currently performing segmentation of MRI Images. Just enquiring if I can open two MRI sequences (DWI and ADC) at the same time and segment the tumour on both sequence side by side.

---

## [How do various slicers encode the origin for their coordinate system?](https://discourse.slicer.org/t/how-do-various-slicers-encode-the-origin-for-their-coordinate-system/32792)

<div class="topic-metadata">

**Author:** [@Ahstark](https://discourse.slicer.org/u/Ahstark)\
**Replies:** 3\
**Last updated:** [November 14, 2023, 3:37am UTC](https://discourse.slicer.org/t/how-do-various-slicers-encode-the-origin-for-their-coordinate-system/32792 "2023-11-14T03:37:21Z")

</div>

I am using ITK-Snap’s 3D segmentation and exporting as surface mesh. I was wondering how I could “Conserve” the approximate coordinates for a specific pixel on the original object. That way I can choose a pixel with an (…

---

## [Problems using ImportOsirixROI from the Sandbox extension](https://discourse.slicer.org/t/problems-using-importosirixroi-from-the-sandbox-extension/31406)

<div class="topic-metadata">

**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 7\
**Last updated:** [November 13, 2023, 9:32pm UTC](https://discourse.slicer.org/t/problems-using-importosirixroi-from-the-sandbox-extension/31406 "2023-11-13T21:32:11Z")

</div>

I’ve just had a conversation with Dr. Ron Summers from NCI, who has been trying to use the ImportOsirixROI function from the Sandbox extension. It is failing with the following error: "\[...\]/AppData/Local/slicer.org/Sli…

---

## [Running python file in Slicer on Mac ](https://discourse.slicer.org/t/running-python-file-in-slicer-on-mac/24356)

<div class="topic-metadata">

**Author:** [@ashuashu](https://discourse.slicer.org/u/ashuashu)\
**Replies:** 11\
**Last updated:** [November 13, 2023, 7:34pm UTC](https://discourse.slicer.org/t/running-python-file-in-slicer-on-mac/24356 "2023-11-13T19:34:21Z")

</div>

Can anyone help me with the commands here? I want to run a deep learning model in the 3D slicer. I have the file on my desktop. I tried to run it on a mac terminal as well as on 3D-Slicer. I am not able to proceed furthe…

---

## [New feature: Support regularization transform hardening in DICOM Scalar plugin](https://discourse.slicer.org/t/new-feature-support-regularization-transform-hardening-in-dicom-scalar-plugin/32772)

<div class="topic-metadata">

**Author:** [@Davide\_Punzo](https://discourse.slicer.org/u/Davide_Punzo)\
**Replies:** 0\
**Last updated:** [November 13, 2023, 8:30am UTC](https://discourse.slicer.org/t/new-feature-support-regularization-transform-hardening-in-dicom-scalar-plugin/32772 "2023-11-13T08:30:17Z")

</div>

Support for regularization transform hardening in DICOM Scalar plugin has been added in commit If selected, the transform is hardened automatically at the loading time of the DICOM. The default behavior is still the…

---

## [Issue with dose comparison](https://discourse.slicer.org/t/issue-with-dose-comparison/32398)

<div class="topic-metadata">

**Author:** [@yasaman\_kiumarsi](https://discourse.slicer.org/u/yasaman_kiumarsi)\
**Replies:** 5\
**Last updated:** [November 13, 2023, 11:13am UTC](https://discourse.slicer.org/t/issue-with-dose-comparison/32398 "2023-11-13T11:13:16Z")

</div>

Operating system: windows10 Slicer version:5.2.2 Expected behavior: Actual behavior: When I click dose comparison, the software closes after a few seconds.

---

## [Remove Pixel Medical from slicer.org commercial use page](https://discourse.slicer.org/t/remove-pixel-medical-from-slicer-org-commercial-use-page/32715)

<div class="topic-metadata">

**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 2\
**Last updated:** [November 13, 2023, 11:05am UTC](https://discourse.slicer.org/t/remove-pixel-medical-from-slicer-org-commercial-use-page/32715 "2023-11-13T11:05:20Z")

</div>

Hi @jcfr @Sam\_Horvath, Not sure who can actually edit the website content, but I’d like to request that Pixel Medical is removed from this page The linked website will go offline shortly. Thank you very much!

---

## [extractorGLCM.execute()](https://discourse.slicer.org/t/extractorglcm-execute/32775)

<div class="topic-metadata">

**Author:** [@Tomas\_Korinek](https://discourse.slicer.org/u/Tomas_Korinek)\
**Replies:** 0\
**Last updated:** [November 13, 2023, 10:15am UTC](https://discourse.slicer.org/t/extractorglcm-execute/32775 "2023-11-13T10:15:31Z")

</div>

Hello everybody. I would love to use your genius ideas and asking for a help. This is my code for radiomics extraction: Img,Mask = PyrexReader.Img\_Bimask(img\_path,rtstruct\_path,ROI) extractorFO = radiomics.first…

---

## [4D ITK image to vtkMRMLGridTransformNode](https://discourse.slicer.org/t/4d-itk-image-to-vtkmrmlgridtransformnode/741)

<div class="topic-metadata">

**Author:** [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Replies:** 10\
**Last updated:** [November 13, 2023, 8:59am UTC](https://discourse.slicer.org/t/4d-itk-image-to-vtkmrmlgridtransformnode/741 "2023-11-13T08:59:32Z")

</div>

Hi all, I have a displacement field “field.nii” that I need to convert from RAS to LPS so that I can use it in Slicer. What I’m doing now is: Read the file with SimpleITK Modify the data Save it Load it with slicer.ut…

---

## [Uneven slice thickness](https://discourse.slicer.org/t/uneven-slice-thickness/6442)

<div class="topic-metadata">

**Author:** [@prorai](https://discourse.slicer.org/u/prorai)\
**Replies:** 11\
**Last updated:** [November 13, 2023, 8:48am UTC](https://discourse.slicer.org/t/uneven-slice-thickness/6442 "2023-11-13T08:48:05Z")

</div>

Any Solution for this??

---

## [Slicer loads wrong image spacing](https://discourse.slicer.org/t/slicer-loads-wrong-image-spacing/453)

<div class="topic-metadata">

**Author:** [@Shilpa\_Ananth](https://discourse.slicer.org/u/Shilpa_Ananth)\
**Replies:** 24\
**Last updated:** [November 13, 2023, 8:44am UTC](https://discourse.slicer.org/t/slicer-loads-wrong-image-spacing/453 "2023-11-13T08:44:20Z")

</div>

Operating system: Windows 64 bit Slicer version: 4.6.2 Expected behavior: My .dcm file has clear values under the Pixel spacing and the Slice thickness,spacing between slices tags. So these values must be loaded onto ima…

---

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

<div class="topic-metadata">

**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")

</div>

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…

---

## [Understanding CT Image spacing and Acquisition geometry regularization](https://discourse.slicer.org/t/understanding-ct-image-spacing-and-acquisition-geometry-regularization/19001)

<div class="topic-metadata">

**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 5\
**Last updated:** [November 13, 2023, 8:37am UTC](https://discourse.slicer.org/t/understanding-ct-image-spacing-and-acquisition-geometry-regularization/19001 "2023-11-13T08:37:23Z")

</div>

Dear all, "Images are not equally spaced (a difference of 0.6 vs 0.3 was detected)’ Why does this error occur? What causes the acquisition of acquired irregular geometry? is it something to do with CT machine, protocol…

---

## [Dicom File Loading Spacing](https://discourse.slicer.org/t/dicom-file-loading-spacing/5469)

<div class="topic-metadata">

**Author:** [@epdawson](https://discourse.slicer.org/u/epdawson)\
**Replies:** 5\
**Last updated:** [November 13, 2023, 8:31am UTC](https://discourse.slicer.org/t/dicom-file-loading-spacing/5469 "2023-11-13T08:31:01Z")

</div>

Two Questions: I have dicom files from MRI which have all necessary metadata, however, only some of the files are consecutive, while others are skipped in between (i.e Dicom 001, Dicom 002, Dicom 007, etc.) The ImageP…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=128)

[Next page](https://discourse.slicer.org/c/support/11.md?page=130)