# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=121

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

**Page:** 122

---

## [Command 'elastix' died with \<Signals.SIGABRT: 6\>.](https://discourse.slicer.org/t/command-elastix-died-with-signals-sigabrt-6/32970)

<div class="topic-metadata">

**Author:** [@Franci](https://discourse.slicer.org/u/Franci)\
**Replies:** 8\
**Last updated:** [January 1, 2024, 5:55pm UTC](https://discourse.slicer.org/t/command-elastix-died-with-signals-sigabrt-6/32970 "2024-01-01T17:55:58Z")

</div>

Hi, I am using a MacBook and Slicer 5.5.0 First I had many issues to find a version that allowed the SlicerElastix downloading. Now when I put my inputs brain files and output + specify the active volume and the looku…

---

## [How to Fuse image SPECT and CTA](https://discourse.slicer.org/t/how-to-fuse-image-spect-and-cta/16814)

<div class="topic-metadata">

**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 19\
**Last updated:** [January 1, 2024, 1:45pm UTC](https://discourse.slicer.org/t/how-to-fuse-image-spect-and-cta/16814 "2024-01-01T13:45:16Z")

</div>

Operating system: windows Slicer version: 4.13 Expected behavior: Actual behavior: anyone can help me with how to fuse image SPECT with CT Abdomen? That is because my spect image inn 4D(one image), while my CTA has (…

---

## [Issue with DICOM to Nifti Conversion](https://discourse.slicer.org/t/issue-with-dicom-to-nifti-conversion/33151)

<div class="topic-metadata">

**Author:** [@Shovon\_Ahmed](https://discourse.slicer.org/u/Shovon_Ahmed)\
**Replies:** 5\
**Last updated:** [December 31, 2023, 6:54am UTC](https://discourse.slicer.org/t/issue-with-dicom-to-nifti-conversion/33151 "2023-12-31T06:54:22Z")

</div>

I am trying to convert Dicom files to Nifti. But after conversion, I see a huge change in intensity (2nd image). I have also tried SimpleITK library bias correction. But the outcomes are the same. Would anyone explain w…

---

## [Maximum distance python code](https://discourse.slicer.org/t/maximum-distance-python-code/33541)

<div class="topic-metadata">

**Author:** [@sima](https://discourse.slicer.org/u/sima)\
**Replies:** 1\
**Last updated:** [December 31, 2023, 4:24am UTC](https://discourse.slicer.org/t/maximum-distance-python-code/33541 "2023-12-31T04:24:07Z")

</div>

I need some help! I have two models: skin and PTV I need a Python code to calculate the maximum distance between these two models in my desired direction or thanks a lot

---

## [Relationship between dcm xyz coordinate and nifti xyz coordinate](https://discourse.slicer.org/t/relationship-between-dcm-xyz-coordinate-and-nifti-xyz-coordinate/33570)

<div class="topic-metadata">

**Author:** [@vidasun](https://discourse.slicer.org/u/vidasun)\
**Replies:** 0\
**Last updated:** [December 30, 2023, 1:50pm UTC](https://discourse.slicer.org/t/relationship-between-dcm-xyz-coordinate-and-nifti-xyz-coordinate/33570 "2023-12-30T13:50:37Z")

</div>

Hi Everyone! I am dealing with converting the dcm world system coordinate to MNI space coordinate. I can get the transformation matrix of nifti to MNI by FSL FLIRT. However, I’m quite confused about the relationship bet…

---

## [Brachytherapy treatment planning](https://discourse.slicer.org/t/brachytherapy-treatment-planning/28652)

<div class="topic-metadata">

**Author:** [@ferhue](https://discourse.slicer.org/u/ferhue)\
**Replies:** 0\
**Last updated:** [March 29, 2023, 12:44pm UTC](https://discourse.slicer.org/t/brachytherapy-treatment-planning/28652 "2023-03-29T12:44:48Z")

</div>

For teaching / academic / research purposes, it would be quite nice to have a basic treatment planning system for brachytherapy seeds. Note: I am cross-posting this from Create Brachy treatment planning module · Issue #…

---

## [CTA Brain Extraction / Skull Stripping](https://discourse.slicer.org/t/cta-brain-extraction-skull-stripping/30427)

<div class="topic-metadata">

**Author:** [@Arpan\_Gyawali](https://discourse.slicer.org/u/Arpan_Gyawali)\
**Replies:** 6\
**Last updated:** [December 29, 2023, 12:44am UTC](https://discourse.slicer.org/t/cta-brain-extraction-skull-stripping/30427 "2023-12-29T00:44:27Z")

</div>

I have a task of extracting Brain or removing skull from a brain CTA scans. To train the model first of all i need to label the mask. I am using 3D slicer segment editor for it. The process I am following is as explained…

---

## [Lobes of the brain segmentation from MRI images (T1)](https://discourse.slicer.org/t/lobes-of-the-brain-segmentation-from-mri-images-t1/25337)

<div class="topic-metadata">

**Author:** [@agatte](https://discourse.slicer.org/u/agatte)\
**Replies:** 3\
**Last updated:** [December 29, 2023, 4:37am UTC](https://discourse.slicer.org/t/lobes-of-the-brain-segmentation-from-mri-images-t1/25337 "2023-12-29T04:37:01Z")

</div>

Hello, I would like to ask you if there is something any tool or module extension to segment lobes of the brain from MRI ?

---

## [intensity correction and spatial normalization](https://discourse.slicer.org/t/intensity-correction-and-spatial-normalization/33548)

<div class="topic-metadata">

**Author:** [@zhudao176](https://discourse.slicer.org/u/zhudao176)\
**Replies:** 1\
**Last updated:** [December 28, 2023, 6:58pm UTC](https://discourse.slicer.org/t/intensity-correction-and-spatial-normalization/33548 "2023-12-28T18:58:05Z")

</div>

Operating system:windows11 Slicer version:5.5.0 Expected behavior: I want to use 3D slicer to automatically delineate the striatum from brain PET/MRI data and obtain radiomics data, but preprocessing is required befo…

---

## [Generate tubes with markups to model](https://discourse.slicer.org/t/generate-tubes-with-markups-to-model/33542)

<div class="topic-metadata">

**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 3\
**Last updated:** [December 28, 2023, 6:07pm UTC](https://discourse.slicer.org/t/generate-tubes-with-markups-to-model/33542 "2023-12-28T18:07:10Z")

</div>

Hi to everyone. At this moment I’m struggling with markupstomodel module, which implements some handsome functions as could be generate tubes from markups. In my first attemp I achieve a fancy solution touching the par…

---

## [Total Segmentator error](https://discourse.slicer.org/t/total-segmentator-error/33547)

<div class="topic-metadata">

**Author:** [@mohamed\_tolba](https://discourse.slicer.org/u/mohamed_tolba)\
**Replies:** 1\
**Last updated:** [December 28, 2023, 5:33pm UTC](https://discourse.slicer.org/t/total-segmentator-error/33547 "2023-12-28T17:33:14Z")

</div>

Hello slicer community. I trying to segment the maxilla and the mandible using total segmentator I get this message " Failed to compute results. Command '\[‘C:/Users/PC/AppData/Local/slicer.org/Slicer 5.4.0/bin/…/bin\\Pyth…

---

## [Slice thickness](https://discourse.slicer.org/t/slice-thickness/20117)

<div class="topic-metadata">

**Author:** [@henrysmith123](https://discourse.slicer.org/u/henrysmith123)\
**Replies:** 5\
**Last updated:** [December 28, 2023, 5:00pm UTC](https://discourse.slicer.org/t/slice-thickness/20117 "2023-12-28T17:00:12Z")

</div>

How can I change the thickness of the CBCT slice for viewing? I’m talking about a function that is in all programs for viewing CT, where I can adjust the slice thickness, for example, 2mm, and still in the 2mm area they …

---

## [Open dicom libraries](https://discourse.slicer.org/t/open-dicom-libraries/32179)

<div class="topic-metadata">

**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 9\
**Last updated:** [December 28, 2023, 3:32pm UTC](https://discourse.slicer.org/t/open-dicom-libraries/32179 "2023-12-28T15:32:32Z")

</div>

Hi everyone! I’d like to get a free and open dicom of a full body and despite the number of results appearing from a google search, I couldn’t find any complete and CCO dicom. The purpose is to use as reference for com…

---

## [Conversion of FA (Fractional Anisotropy) map to DICOM failing](https://discourse.slicer.org/t/conversion-of-fa-fractional-anisotropy-map-to-dicom-failing/33294)

<div class="topic-metadata">

**Author:** [@snnstuff](https://discourse.slicer.org/u/snnstuff)\
**Replies:** 5\
**Last updated:** [December 28, 2023, 4:02am UTC](https://discourse.slicer.org/t/conversion-of-fa-fractional-anisotropy-map-to-dicom-failing/33294 "2023-12-28T04:02:55Z")

</div>

I’m trying to convert a FA map in nifti format to DICOM format. I tried intermediary steps of converting the nifti file to NRRD first (and TIF), but the output has no contrast. DICOM files are created, but the image co…

---

## [I haven't find the Radiomics on my new Mac](https://discourse.slicer.org/t/i-havent-find-the-radiomics-on-my-new-mac/33535)

<div class="topic-metadata">

**Author:** [@taehyeongkim9010](https://discourse.slicer.org/u/taehyeongkim9010)\
**Replies:** 3\
**Last updated:** [December 28, 2023, 2:21am UTC](https://discourse.slicer.org/t/i-havent-find-the-radiomics-on-my-new-mac/33535 "2023-12-28T02:21:02Z")

</div>

Operating system: MAC M3 Sonoma 14.1 Slicer version: 5.6.1 (Mac version) Expected behavior: Actual behavior: Recently, Im install the python 3.12 with pycham, also installed the slicer v.5.6.1 but, Im not found the …

---

## [【Paid】Is there a plug-in or Technical solutions in Slicer that can provide temperature measurement function using ultrasonic equipment?](https://discourse.slicer.org/t/paid-is-there-a-plug-in-or-technical-solutions-in-slicer-that-can-provide-temperature-measurement-function-using-ultrasonic-equipment/33438)

<div class="topic-metadata">

**Author:** [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Replies:** 2\
**Last updated:** [December 28, 2023, 1:36am UTC](https://discourse.slicer.org/t/paid-is-there-a-plug-in-or-technical-solutions-in-slicer-that-can-provide-temperature-measurement-function-using-ultrasonic-equipment/33438 "2023-12-28T01:36:42Z")

</div>

Our customer wants to add a function of using ultrasonic equipment to measure temperature, but I don’t know how to do it. If there is a plug-in or technical solution that can solve this problem, our customer is willing t…

---

## [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)

<div class="topic-metadata">

**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")

</div>

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…

---

## [Stop code execution until Event](https://discourse.slicer.org/t/stop-code-execution-until-event/33532)

<div class="topic-metadata">

**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 1\
**Last updated:** [December 27, 2023, 6:30pm UTC](https://discourse.slicer.org/t/stop-code-execution-until-event/33532 "2023-12-27T18:30:50Z")

</div>

Hi all :slight\_smile: On this time I’m interested in automatize some process, related with centerline quantification and data related with it. In my code I have to put some fiducial (that can not be set before), and wi…

---

## [Window closes when using SegmentGeometry (from SlicerBiomech), some timer after hiting the "apply" button](https://discourse.slicer.org/t/window-closes-when-using-segmentgeometry-from-slicerbiomech-some-timer-after-hiting-the-apply-button/33514)

<div class="topic-metadata">

**Author:** [@Henry\_Lopes](https://discourse.slicer.org/u/Henry_Lopes)\
**Replies:** 2\
**Last updated:** [December 27, 2023, 5:09am UTC](https://discourse.slicer.org/t/window-closes-when-using-segmentgeometry-from-slicerbiomech-some-timer-after-hiting-the-apply-button/33514 "2023-12-27T05:09:53Z")

</div>

The SegmentGeometry module (from the SlicerBiomech extension) doesn’t work, even with sample data. This is what happens: I select the volume and the segment, with simple parameters; I click the “apply” button; The wind…

---

## [Unable to paint under rhe segmentation module](https://discourse.slicer.org/t/unable-to-paint-under-rhe-segmentation-module/33526)

<div class="topic-metadata">

**Author:** [@Michelle\_Cataldo](https://discourse.slicer.org/u/Michelle_Cataldo)\
**Replies:** 2\
**Last updated:** [December 27, 2023, 1:59am UTC](https://discourse.slicer.org/t/unable-to-paint-under-rhe-segmentation-module/33526 "2023-12-27T01:59:45Z")

</div>

Hello guys, 'im trying to paint the area on the ROI I determined but, it wont segment the area. it “erase” itself whenever I stop holding and dragging the mouse. I cant draw anything too. I could segment without problems…

---

## [DICOMDIR file conversion](https://discourse.slicer.org/t/dicomdir-file-conversion/33525)

<div class="topic-metadata">

**Author:** [@anamcastano](https://discourse.slicer.org/u/anamcastano)\
**Replies:** 1\
**Last updated:** [December 26, 2023, 7:26pm UTC](https://discourse.slicer.org/t/dicomdir-file-conversion/33525 "2023-12-26T19:26:31Z")

</div>

Hi all Could anyone help me to manage with DICOMDIR instead of DICOM files to create NRRD, DWI and DTI? Is there any converter DICOMDIR to DICOM? Thanks in advance

---

## [How do you change the slice thickness and add it to a module panel?](https://discourse.slicer.org/t/how-do-you-change-the-slice-thickness-and-add-it-to-a-module-panel/33522)

<div class="topic-metadata">

**Author:** [@ddii](https://discourse.slicer.org/u/ddii)\
**Replies:** 0\
**Last updated:** [December 26, 2023, 12:23am UTC](https://discourse.slicer.org/t/how-do-you-change-the-slice-thickness-and-add-it-to-a-module-panel/33522 "2023-12-26T00:23:19Z")

</div>

How do you change the slice thickness and add it to a module panel? Thanks!

---

## [How do you add \[Volume Rendering function\] to the custom module panel?](https://discourse.slicer.org/t/how-do-you-add-volume-rendering-function-to-the-custom-module-panel/33521)

<div class="topic-metadata">

**Author:** [@ddii](https://discourse.slicer.org/u/ddii)\
**Replies:** 0\
**Last updated:** [December 26, 2023, 12:11am UTC](https://discourse.slicer.org/t/how-do-you-add-volume-rendering-function-to-the-custom-module-panel/33521 "2023-12-26T00:11:36Z")

</div>

Is there any way to add volume rendering function into custom module panel? Also wanted to add \[Volume rendering ROI\] with the interaction handle enable (all translation, rotation and scaling enables) to the module p…

---

## [calculate the ADC map from DWI data](https://discourse.slicer.org/t/calculate-the-adc-map-from-dwi-data/33519)

<div class="topic-metadata">

**Author:** [@smati\_wissem](https://discourse.slicer.org/u/smati_wissem)\
**Replies:** 0\
**Last updated:** [December 26, 2023, 12:02am UTC](https://discourse.slicer.org/t/calculate-the-adc-map-from-dwi-data/33519 "2023-12-26T00:02:41Z")

</div>

Hello everyone, it’s been 5 days that I’ve been searching for a solution to my problem, but I haven’t found one. So, I’m reaching out for your help. My question is how to calculate the ADC volume from a DWI volume. Than…

---

## [Double-clicking to zoom in and out](https://discourse.slicer.org/t/double-clicking-to-zoom-in-and-out/33512)

<div class="topic-metadata">

**Author:** [@yuanw](https://discourse.slicer.org/u/yuanw)\
**Replies:** 2\
**Last updated:** [December 25, 2023, 5:36am UTC](https://discourse.slicer.org/t/double-clicking-to-zoom-in-and-out/33512 "2023-12-25T05:36:43Z")

</div>

How to enable the function of double-clicking to zoom in and out? After I updated to 5.6.0, the function of double-clicking to zoom in and out is no longer available.

---

## [Comparison of CBCT images with regard to preoperative and postoperative position and relation](https://discourse.slicer.org/t/comparison-of-cbct-images-with-regard-to-preoperative-and-postoperative-position-and-relation/29033)

<div class="topic-metadata">

**Author:** [@vollmer\_a](https://discourse.slicer.org/u/vollmer_a)\
**Replies:** 3\
**Last updated:** [December 24, 2023, 7:47pm UTC](https://discourse.slicer.org/t/comparison-of-cbct-images-with-regard-to-preoperative-and-postoperative-position-and-relation/29033 "2023-12-24T19:47:49Z")

</div>

Dear colleagues, I work as a facial surgeon at a German university hospital and we would very much like to compare the position of a mandible using CBCT images. This is to compare tumour patients and orthopaedic dysgnat…

---

## [Continous color table for heatmap](https://discourse.slicer.org/t/continous-color-table-for-heatmap/33464)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 9\
**Last updated:** [December 24, 2023, 2:00pm UTC](https://discourse.slicer.org/t/continous-color-table-for-heatmap/33464 "2023-12-24T14:00:03Z")

</div>

We have an image in which the voxel values are the statistical effect sizes ranging from about -0.3 to 0.9. Most of the image is 0s (voxels that didn’t reach significance). I would like to render this image in a way that…

---

## [DICOM browser does not show the count of images in a series](https://discourse.slicer.org/t/dicom-browser-does-not-show-the-count-of-images-in-a-series/33506)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [December 23, 2023, 10:56pm UTC](https://discourse.slicer.org/t/dicom-browser-does-not-show-the-count-of-images-in-a-series/33506 "2023-12-23T22:56:33Z")

</div>

Hi, I built Slicer 66a424d on Linux and recreated the DICOM database. The number of images in the series are not available in the DICOM browser. Thanks for having a look.

---

## [Masking/segmentations disappearing issue](https://discourse.slicer.org/t/masking-segmentations-disappearing-issue/33500)

<div class="topic-metadata">

**Author:** [@ndelgado](https://discourse.slicer.org/u/ndelgado)\
**Replies:** 1\
**Last updated:** [December 22, 2023, 8:15pm UTC](https://discourse.slicer.org/t/masking-segmentations-disappearing-issue/33500 "2023-12-22T20:15:19Z")

</div>

When I am segmenting, sometimes it will disappear on me. I can see it in the 3D area but not in any of slices. Sometimes, this will happen after I apply thresholding, and other times, it appears to occur randomly. Is the…

---

## [Python code exit abnormally. custom plugin development](https://discourse.slicer.org/t/python-code-exit-abnormally-custom-plugin-development/33404)

<div class="topic-metadata">

**Author:** [@IVarha](https://discourse.slicer.org/u/IVarha)\
**Replies:** 4\
**Last updated:** [December 22, 2023, 12:11pm UTC](https://discourse.slicer.org/t/python-code-exit-abnormally-custom-plugin-development/33404 "2023-12-22T12:11:40Z")

</div>

Hello I am developing a plugin for my research and encountering with a problem when I am running certain code. However error is not reproducible when I am running same code on PythonSlicer (built in in slicer). Here I a…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=120)

[Next page](https://discourse.slicer.org/c/support/11.md?page=122)