# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=101

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

**Page:** 102

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## [Export binary mask of the segmentation as jpeg/png](https://discourse.slicer.org/t/export-binary-mask-of-the-segmentation-as-jpeg-png/28256)

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**Author:** [@yoav\_benhaim](https://discourse.slicer.org/u/yoav_benhaim)\
**Replies:** 2\
**Last updated:** [April 18, 2024, 10:06am UTC](https://discourse.slicer.org/t/export-binary-mask-of-the-segmentation-as-jpeg-png/28256 "2024-04-18T10:06:06Z")

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hi! how can I export the segmentation as a binary image? the preference file format is jpeg or png/ but other format can also help thank you

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## [IGT Extensions do not appear in modules sections](https://discourse.slicer.org/t/igt-extensions-do-not-appear-in-modules-sections/35583)

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**Author:** [@Caterina](https://discourse.slicer.org/u/Caterina)\
**Replies:** 0\
**Last updated:** [April 18, 2024, 9:26am UTC](https://discourse.slicer.org/t/igt-extensions-do-not-appear-in-modules-sections/35583 "2024-04-18T09:26:07Z")

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Dear Support, I’m using Slicer version 5.6.1. Although they are correctly installed, SilcerAIGT, SlicerIGTSIO,SlicerIGT and SlicerOpenIGTLInk do not appear in modules sections. So I cannot use them. Any suggestion?Than…

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## [Compare two CBCT volumes](https://discourse.slicer.org/t/compare-two-cbct-volumes/18463)

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**Author:** [@MelanieW](https://discourse.slicer.org/u/MelanieW)\
**Replies:** 4\
**Last updated:** [April 18, 2024, 12:12am UTC](https://discourse.slicer.org/t/compare-two-cbct-volumes/18463 "2024-04-18T00:12:48Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Expected behavior: I would like to compare CBCT volume difference between pre and post bone grafts of the maxilla. I have registered the two original pre and …

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## [Spline Curvature Measurements](https://discourse.slicer.org/t/spline-curvature-measurements/35505)

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**Author:** [@chub](https://discourse.slicer.org/u/chub)\
**Replies:** 4\
**Last updated:** [April 17, 2024, 11:58pm UTC](https://discourse.slicer.org/t/spline-curvature-measurements/35505 "2024-04-17T23:58:26Z")

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Hello! I am attempting to characterize curvature of lung anatomy. I am creating splines down the center of bronchi by placing ~5 equidistant control points (~70mm total length). When looking at the curvature mean and c…

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## [Aligning control points vertically?](https://discourse.slicer.org/t/aligning-control-points-vertically/35566)

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**Author:** [@CanidMorpho](https://discourse.slicer.org/u/CanidMorpho)\
**Replies:** 3\
**Last updated:** [April 17, 2024, 7:55pm UTC](https://discourse.slicer.org/t/aligning-control-points-vertically/35566 "2024-04-17T19:55:08Z")

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Is there a way to perfectly align two control points vertically? More specifically, if I place a landmark beside a tooth on a canid mandible, how can I ensure that a point I place at the bottom of the jaw is perfectly al…

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## [How to shrink mrb file size?](https://discourse.slicer.org/t/how-to-shrink-mrb-file-size/35550)

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**Author:** [@Stuart](https://discourse.slicer.org/u/Stuart)\
**Replies:** 6\
**Last updated:** [April 17, 2024, 7:09pm UTC](https://discourse.slicer.org/t/how-to-shrink-mrb-file-size/35550 "2024-04-17T19:09:00Z")

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Operating system: OSX Slicer version:5.6.2 Expected behavior: small file Actual behavior: large file

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## [Load three PET/CTs in a separate window](https://discourse.slicer.org/t/load-three-pet-cts-in-a-separate-window/35551)

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**Author:** [@rkraaijveld](https://discourse.slicer.org/u/rkraaijveld)\
**Replies:** 1\
**Last updated:** [April 17, 2024, 5:54pm UTC](https://discourse.slicer.org/t/load-three-pet-cts-in-a-separate-window/35551 "2024-04-17T17:54:08Z")

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Hi! I am making an extension where I load three CT images into the separate windows (Green, Red and Yellow). If available, I would also like to load the PET scan as foreground. Loading the three CT images is successful,…

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## [How can i change the patient information in DICOM files using 3D Slicer during import?](https://discourse.slicer.org/t/how-can-i-change-the-patient-information-in-dicom-files-using-3d-slicer-during-import/35451)

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**Author:** [@Jake1](https://discourse.slicer.org/u/Jake1)\
**Replies:** 3\
**Last updated:** [April 17, 2024, 5:37pm UTC](https://discourse.slicer.org/t/how-can-i-change-the-patient-information-in-dicom-files-using-3d-slicer-during-import/35451 "2024-04-17T17:37:13Z")

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Operating system: win 10 Slicer version: 5.6.1 For research purposes, I would like to de-identify the CBCT files I have. Does anyone know how to do this? Sincere thanks!

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## [Contact Position Estimator](https://discourse.slicer.org/t/contact-position-estimator/35565)

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**Author:** [@Bobby](https://discourse.slicer.org/u/Bobby)\
**Replies:** 0\
**Last updated:** [April 17, 2024, 5:24pm UTC](https://discourse.slicer.org/t/contact-position-estimator/35565 "2024-04-17T17:24:50Z")

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Hi, I tried installing the SEEGA based on the instruction given in this page “Installation Guide · mnarizzano/SEEGA Wiki · GitHub”. When I open the module contact position estimator, it didn’t show the option for loadin…

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## [I am unable to upload .vti file (DICOM) heart CT/MRI data in 3D slicer5.6.1 on Mac](https://discourse.slicer.org/t/i-am-unable-to-upload-vti-file-dicom-heart-ct-mri-data-in-3d-slicer5-6-1-on-mac/35560)

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**Author:** [@nikita\_singh](https://discourse.slicer.org/u/nikita_singh)\
**Replies:** 0\
**Last updated:** [April 17, 2024, 2:08pm UTC](https://discourse.slicer.org/t/i-am-unable-to-upload-vti-file-dicom-heart-ct-mri-data-in-3d-slicer5-6-1-on-mac/35560 "2024-04-17T14:08:26Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Change SubjectHierarchy name](https://discourse.slicer.org/t/change-subjecthierarchy-name/35556)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 3\
**Last updated:** [April 17, 2024, 1:29pm UTC](https://discourse.slicer.org/t/change-subjecthierarchy-name/35556 "2024-04-17T13:29:16Z")

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Hi to everyone. Today I’m trying to change the SubjectHierarchy name using Python code. My goal is the next one: Actual name: VAL22^Val22(AW388… Real Name: VAL22 Thanks a lot!

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## [US transducer path tracker](https://discourse.slicer.org/t/us-transducer-path-tracker/35526)

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**Author:** [@avimo1](https://discourse.slicer.org/u/avimo1)\
**Replies:** 4\
**Last updated:** [April 17, 2024, 7:05am UTC](https://discourse.slicer.org/t/us-transducer-path-tracker/35526 "2024-04-17T07:05:42Z")

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Hi, I am new to 3D slicer, please be patient we me. It will be delightful to know if there is a way to load the US probe pathway as a separate file to the US image files batch, if there is a thread about this topic he…

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## [How Can I measure Pores in the fibers?](https://discourse.slicer.org/t/how-can-i-measure-pores-in-the-fibers/27769)

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**Author:** [@Poorya\_Esmaili](https://discourse.slicer.org/u/Poorya_Esmaili)\
**Replies:** 3\
**Last updated:** [April 17, 2024, 1:46am UTC](https://discourse.slicer.org/t/how-can-i-measure-pores-in-the-fibers/27769 "2024-04-17T01:46:12Z")

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Hello I want to analyze poros in the fiber. My intention is that in the poros section of the fiber what is the size of sphere that I can fit in the each pore are. is it possible in 3D slicer?? I would be appreciated it…

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## [Importing a template with empty segmentation](https://discourse.slicer.org/t/importing-a-template-with-empty-segmentation/35520)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 5:01pm UTC](https://discourse.slicer.org/t/importing-a-template-with-empty-segmentation/35520 "2024-04-16T17:01:26Z")

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Dear all, I have a question that has come up before and my apologies if there the answers I am looking for elsewhere. My query is related to a previous post: Segment Editor color/name template - Support - 3D Slicer Co…

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## [2D/3D fill tool](https://discourse.slicer.org/t/2d-3d-fill-tool/2682)

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**Author:** [@Leon](https://discourse.slicer.org/u/Leon)\
**Replies:** 25\
**Last updated:** [April 16, 2024, 4:46pm UTC](https://discourse.slicer.org/t/2d-3d-fill-tool/2682 "2024-04-16T16:46:15Z")

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Hi, Just a simple question for which I hope there is a simple answer. I’m exploring 3DSlicer as a possible alternative to Mimics. To do this I’m segmenting a femur that I already segmented with Mimics to compare the ou…

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## [About dicom or nifti standardization](https://discourse.slicer.org/t/about-dicom-or-nifti-standardization/35517)

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**Author:** [@Berk\_Gezgin](https://discourse.slicer.org/u/Berk_Gezgin)\
**Replies:** 4\
**Last updated:** [April 16, 2024, 4:03pm UTC](https://discourse.slicer.org/t/about-dicom-or-nifti-standardization/35517 "2024-04-16T16:03:57Z")

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Hello. I have 2 different nifti. One of them comes in the same way on the same axes as the original dicom. The other one is inverted or axial, sagittal displaced. What should I do to apply a standardization? Is there a …

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## [Installing SlicerJupyter causes Slicer to crash](https://discourse.slicer.org/t/installing-slicerjupyter-causes-slicer-to-crash/32082)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 3\
**Last updated:** [April 16, 2024, 3:58pm UTC](https://discourse.slicer.org/t/installing-slicerjupyter-causes-slicer-to-crash/32082 "2024-04-16T15:58:13Z")

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When I install SlicerJupyter on my MacBook (OS Monterey, 12.5.1) and restart, the application repeatedly crashes during launch. I can fix this by deleting the extension files from the application. I have tried this for …

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## [Misalignment between Freesurfer brain segmentation and original T1 images](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524)

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**Author:** [@pablomac7](https://discourse.slicer.org/u/pablomac7)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 12:20pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524 "2024-04-16T12:20:44Z")

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Slicer version: 5.6.1 Hello, I am having problems when exporting a brain segmentation as a .seg.nrrd file, previously imported into 3D Slicer from Freesurfer. When I import the segmentation and the original MRI images …

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## [Encountering error when running Auto3dgm extension](https://discourse.slicer.org/t/encountering-error-when-running-auto3dgm-extension/35511)

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**Author:** [@jamie.wiener](https://discourse.slicer.org/u/jamie.wiener)\
**Replies:** 1\
**Last updated:** [April 16, 2024, 11:22am UTC](https://discourse.slicer.org/t/encountering-error-when-running-auto3dgm-extension/35511 "2024-04-16T11:22:09Z")

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Hi, everyone— I recently installed the Auto3dgm extension and have been encountering this error upon importing my data: ImportError: cannot import name ‘square’ from ‘scipy’ (C:\\Users\\hijam\\AppData\\Local\\slicer.org\\Sli…

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## [Volume rendering function](https://discourse.slicer.org/t/volume-rendering-function/35499)

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**Author:** [@capucinelab](https://discourse.slicer.org/u/capucinelab)\
**Replies:** 1\
**Last updated:** [April 16, 2024, 9:11am UTC](https://discourse.slicer.org/t/volume-rendering-function/35499 "2024-04-16T09:11:02Z")

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Automatic translation: Good morning, I would like to use this function to have a 3D vision of skull scans, in order to crop them and do affine registration. However, the volume is displayed perhaps once in 5, without e…

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## [ALPS index calculation- DTI sequence](https://discourse.slicer.org/t/alps-index-calculation-dti-sequence/28721)

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**Author:** [@emin](https://discourse.slicer.org/u/emin)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 7:08am UTC](https://discourse.slicer.org/t/alps-index-calculation-dti-sequence/28721 "2024-04-16T07:08:59Z")

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hi, i need the calculate ALPS index for DTI sequence, anyone can describe steps? help me

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## [Coloring Segments](https://discourse.slicer.org/t/coloring-segments/35497)

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**Author:** [@ljuno](https://discourse.slicer.org/u/ljuno)\
**Replies:** 1\
**Last updated:** [April 15, 2024, 9:27pm UTC](https://discourse.slicer.org/t/coloring-segments/35497 "2024-04-15T21:27:42Z")

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Hello, I am fairly new to 3D slicer and wanted to know if I could use different colors to highlight the nerves in my project: I made the whole brain as one segment, so I am unable to just change the color of the speci…

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## [SPHARM-PDM correspondence imrpovement](https://discourse.slicer.org/t/spharm-pdm-correspondence-imrpovement/35503)

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**Author:** [@samia](https://discourse.slicer.org/u/samia)\
**Replies:** 0\
**Last updated:** [April 15, 2024, 5:00pm UTC](https://discourse.slicer.org/t/spharm-pdm-correspondence-imrpovement/35503 "2024-04-15T17:00:11Z")

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Hello , i have a question about the correspondence improvement in SPHARM- PDM module after adding the landmarks i got two folders that contains the aligned models and the rotated sphere is it possible or how can i check …

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## [Audit Trail for Annotation](https://discourse.slicer.org/t/audit-trail-for-annotation/35496)

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**Author:** [@Shraddha\_Agrawal](https://discourse.slicer.org/u/Shraddha_Agrawal)\
**Replies:** 0\
**Last updated:** [April 15, 2024, 3:29pm UTC](https://discourse.slicer.org/t/audit-trail-for-annotation/35496 "2024-04-15T15:29:35Z")

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Creating an audit trail in a 3D slice tool involves several considerations to ensure it meets the needs of users effectively. Here’s how you might approach implementing this feature: Audit Trail Integration: Integrat…

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## [Bone Segmentation using TotalSegmentor Threshold Slicer 5.6.2](https://discourse.slicer.org/t/bone-segmentation-using-totalsegmentor-threshold-slicer-5-6-2/35357)

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**Author:** [@hmaguile](https://discourse.slicer.org/u/hmaguile)\
**Replies:** 1\
**Last updated:** [April 15, 2024, 7:53am UTC](https://discourse.slicer.org/t/bone-segmentation-using-totalsegmentor-threshold-slicer-5-6-2/35357 "2024-04-15T07:53:32Z")

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Hi, I’ve been on the hunt for the best method to extract ribs from CT scans. It’s not a big deal if other internal parts get included in the process since my goal is to create 3D models of the bones, and study the rib c…

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## [Non-rigid registration of breast MRI in prone position to breast CT in supine position](https://discourse.slicer.org/t/non-rigid-registration-of-breast-mri-in-prone-position-to-breast-ct-in-supine-position/35474)

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**Author:** [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Replies:** 2\
**Last updated:** [April 14, 2024, 3:31am UTC](https://discourse.slicer.org/t/non-rigid-registration-of-breast-mri-in-prone-position-to-breast-ct-in-supine-position/35474 "2024-04-14T03:31:07Z")

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Hello everyone. In breast cancer diagnosis, patients undergo breast MRI in a prone position. However, the surgery is conducted in a supine position. Due to gravity, the breast deforms from the prone to the supine positio…

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## [NameError: name 'slicer' is not defined](https://discourse.slicer.org/t/nameerror-name-slicer-is-not-defined/23677)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 2\
**Last updated:** [April 13, 2024, 3:46pm UTC](https://discourse.slicer.org/t/nameerror-name-slicer-is-not-defined/23677 "2024-04-13T15:46:00Z")

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Windows 10, Slicer 5.0.2, jupyter server 5.0 NameError: name ‘slicer’ is not defined Please refer to this screenshot: Capture — ImgBB In the cmd history, we can see that the scene file is loaded successfully, ho…

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## [Lung cancer segmentation ](https://discourse.slicer.org/t/lung-cancer-segmentation/35464)

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**Author:** [@salma\_el](https://discourse.slicer.org/u/salma_el)\
**Replies:** 0\
**Last updated:** [April 12, 2024, 10:08pm UTC](https://discourse.slicer.org/t/lung-cancer-segmentation/35464 "2024-04-12T22:08:52Z")

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Hi, I am working on a radiomic study, and I really need an automatic extension for lung cancer segmentation. I tried manual segmentation, but it takes a lot of time, and it’s not robust. I need answers as soon as possibl…

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## [Import nifti segmentation files](https://discourse.slicer.org/t/import-nifti-segmentation-files/35423)

<div class="topic-metadata">

**Author:** [@ssfzzzc](https://discourse.slicer.org/u/ssfzzzc)\
**Replies:** 3\
**Last updated:** [April 12, 2024, 6:34pm UTC](https://discourse.slicer.org/t/import-nifti-segmentation-files/35423 "2024-04-12T18:34:08Z")

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I trained a CT segmentation model that saves its result (n x 512 x 512 binary label map) into a .nii.gz file. I tried to import the segmentation file into slicer, but the segmentation mask always appeared outside the C…

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## [Measuring pore diameter automatically](https://discourse.slicer.org/t/measuring-pore-diameter-automatically/35458)

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**Author:** [@ahmad\_alminnawi](https://discourse.slicer.org/u/ahmad_alminnawi)\
**Replies:** 0\
**Last updated:** [April 12, 2024, 1:40pm UTC](https://discourse.slicer.org/t/measuring-pore-diameter-automatically/35458 "2024-04-12T13:40:26Z")

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Hello, I have CT scans of porous tissues and I created segmentation for my ROI. I usually have multiple pores even if the ROI is small (as in the picture) and I want to measure the diameter of these pores. I saw there …

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