# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=189

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

**Page:** 190

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## [Grey Scale Color Inversion not Saving/Exporting in DICOM](https://discourse.slicer.org/t/grey-scale-color-inversion-not-saving-exporting-in-dicom/26759)

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**Author:** [@Bethrg](https://discourse.slicer.org/u/Bethrg)\
**Replies:** 1\
**Last updated:** [December 16, 2022, 1:44am UTC](https://discourse.slicer.org/t/grey-scale-color-inversion-not-saving-exporting-in-dicom/26759 "2022-12-16T01:44:25Z")

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Hello, I have an MRI DICOM image stack for which I need to invert the colors (to make it appear like a CT), save the change, and then export that “negative”, also as a DICOM to use in another treatment planning software…

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## [Scaling radiographs](https://discourse.slicer.org/t/scaling-radiographs/26750)

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**Author:** [@anromero](https://discourse.slicer.org/u/anromero)\
**Replies:** 2\
**Last updated:** [December 15, 2022, 8:59pm UTC](https://discourse.slicer.org/t/scaling-radiographs/26750 "2022-12-15T20:59:47Z")

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I am working with radiographs of patient heads with a known scale of 5.7143 pixels/mm and 1.2 magnification. Once I upload the image to 3D Slicer, I am having trouble figuring out how to input this information so that we…

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## [How to create a Python Module in slicer from a python script?](https://discourse.slicer.org/t/how-to-create-a-python-module-in-slicer-from-a-python-script/26747)

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**Author:** [@bremsstrahlung](https://discourse.slicer.org/u/bremsstrahlung)\
**Replies:** 1\
**Last updated:** [December 15, 2022, 4:27pm UTC](https://discourse.slicer.org/t/how-to-create-a-python-module-in-slicer-from-a-python-script/26747 "2022-12-15T16:27:08Z")

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I have a python script that i paste in the Python Interactive console to achieve whatever task that i wish to. How do i convert this code into a simple module where the user just clicks on the module and the code runs? E…

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## [The layer using segmentEditor reported an error while importing dicom data](https://discourse.slicer.org/t/the-layer-using-segmenteditor-reported-an-error-while-importing-dicom-data/26703)

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**Author:** [@FUFU](https://discourse.slicer.org/u/FUFU)\
**Replies:** 6\
**Last updated:** [December 15, 2022, 2:36pm UTC](https://discourse.slicer.org/t/the-layer-using-segmenteditor-reported-an-error-while-importing-dicom-data/26703 "2022-12-15T14:36:56Z")

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When importing dicom data, the segmentEditor function was found to be faulty. When you use Paint and Erase, it will go to the next layer, not the current one. The same goes for using slicer’s built-in segment…

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## [When importing data on 3dslicer version 5.0, the data displayed is different from the original data](https://discourse.slicer.org/t/when-importing-data-on-3dslicer-version-5-0-the-data-displayed-is-different-from-the-original-data/26702)

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**Author:** [@FUFU](https://discourse.slicer.org/u/FUFU)\
**Replies:** 5\
**Last updated:** [December 15, 2022, 2:08pm UTC](https://discourse.slicer.org/t/when-importing-data-on-3dslicer-version-5-0-the-data-displayed-is-different-from-the-original-data/26702 "2022-12-15T14:08:01Z")

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For example, when I imported dicom data on 3dslicer on version 4.8, it would show the mark traces of layers 162 to 167. But if I run the same dicom data on version 5.0, it only shows traces of data from layers 163 to…

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## [Offline installation of TotalSegmentator](https://discourse.slicer.org/t/offline-installation-of-totalsegmentator/26735)

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**Author:** [@Augusto](https://discourse.slicer.org/u/Augusto)\
**Replies:** 4\
**Last updated:** [December 14, 2022, 7:48pm UTC](https://discourse.slicer.org/t/offline-installation-of-totalsegmentator/26735 "2022-12-14T19:48:22Z")

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Hello, I have a computer with 3D Slicer, but has no internet connection, therefore to install extensions i have to download them from another computer and passed the folder to the one having 3D Slicer installed. I saw …

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## [More than one rotation slider in transforms module can be non-zero](https://discourse.slicer.org/t/more-than-one-rotation-slider-in-transforms-module-can-be-non-zero/26713)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 2\
**Last updated:** [December 14, 2022, 3:57pm UTC](https://discourse.slicer.org/t/more-than-one-rotation-slider-in-transforms-module-can-be-non-zero/26713 "2022-12-14T15:57:09Z")

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As mentioned in the below comment in another thread, and according to the Transforms module documentation regarding editing: Note: Linear transform edit sliders only show relative translation and rotation because a t…

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## [Shortcut inquiry](https://discourse.slicer.org/t/shortcut-inquiry/26721)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 4\
**Last updated:** [December 14, 2022, 2:03pm UTC](https://discourse.slicer.org/t/shortcut-inquiry/26721 "2022-12-14T14:03:10Z")

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is there a shortcut to move slices during full-screen 3D view? i need to have this view in full screen and move the sagittal or coronal slice. I couldn’t find a shortcut to do that. thanks

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## [Volume Rendering - Lung Vessels segmentation without contrast](https://discourse.slicer.org/t/volume-rendering-lung-vessels-segmentation-without-contrast/26697)

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**Author:** [@Eserval](https://discourse.slicer.org/u/Eserval)\
**Replies:** 5\
**Last updated:** [December 13, 2022, 10:18pm UTC](https://discourse.slicer.org/t/volume-rendering-lung-vessels-segmentation-without-contrast/26697 "2022-12-13T22:18:15Z")

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Hello everyone! I’m working on my doctorate involving quality in lung resections. For that, I’m segmenting some Lung CT without IV contrast. Sometimes I use volume rendering to help the segmentation process (an excellen…

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## [Correction of misaligned slices in cardiac segmentation from MRI image](https://discourse.slicer.org/t/correction-of-misaligned-slices-in-cardiac-segmentation-from-mri-image/26716)

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**Author:** [@bmoscoloni](https://discourse.slicer.org/u/bmoscoloni)\
**Replies:** 1\
**Last updated:** [December 13, 2022, 8:56pm UTC](https://discourse.slicer.org/t/correction-of-misaligned-slices-in-cardiac-segmentation-from-mri-image/26716 "2022-12-13T20:56:45Z")

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Hello, I am currently working on the segmentations from a multi-vendor dataset of CMR of which I have the ED frame and the corresponding segmentation for LV, RV, and myocardium. When uploading both the frame and the seg…

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## [CenterLine strange error - Using \`--no-main--window\`](https://discourse.slicer.org/t/centerline-strange-error-using-no-main-window/26696)

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**Author:** [@lucas\_sd](https://discourse.slicer.org/u/lucas_sd)\
**Replies:** 3\
**Last updated:** [December 13, 2022, 3:22pm UTC](https://discourse.slicer.org/t/centerline-strange-error-using-no-main-window/26696 "2022-12-13T15:22:10Z")

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Hi everybody, Im using the module for obtain the centerline from a segmentation. I created a module wich call the centerline module and it works fine. When I run the same code but using slicer --no-main–window, the prog…

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## [brain segmentation mask](https://discourse.slicer.org/t/brain-segmentation-mask/26711)

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**Author:** [@Albulena\_Bajrami](https://discourse.slicer.org/u/Albulena_Bajrami)\
**Replies:** 1\
**Last updated:** [December 13, 2022, 2:46pm UTC](https://discourse.slicer.org/t/brain-segmentation-mask/26711 "2022-12-13T14:46:10Z")

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Hi I was working on manual segmentation of some kind of lesions in the brain. I have to do one first segmentation on a certain sequence, afterwards have to use the same one and modify it and save as a new NIFTI file. I…

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## [Partial Foot and Ankle scan from CT](https://discourse.slicer.org/t/partial-foot-and-ankle-scan-from-ct/26681)

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**Author:** [@cepehde](https://discourse.slicer.org/u/cepehde)\
**Replies:** 3\
**Last updated:** [December 13, 2022, 4:36am UTC](https://discourse.slicer.org/t/partial-foot-and-ankle-scan-from-ct/26681 "2022-12-13T04:36:08Z")

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Operating system: Windows 10 Pro Slicer version: 5.0.3 Expected behavior: Full View of Foot and Ankle Actual behavior: Small Partial view of Foot and Ankle I have a Foot and Ankle CT scan that only loads a s…

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## [Import Numpy File in as image volume](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 5\
**Last updated:** [December 12, 2022, 10:47pm UTC](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653 "2022-12-12T22:47:35Z")

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I have been working with trying to compress files down to NPY and NPZ files to save binary labelmaps for some of my data. Is there a way to import them into slicer? Every time I try the load data option with it, it doesn…

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## [Resizing description field in the markups control points table](https://discourse.slicer.org/t/resizing-description-field-in-the-markups-control-points-table/26673)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 20\
**Last updated:** [December 12, 2022, 6:32pm UTC](https://discourse.slicer.org/t/resizing-description-field-in-the-markups-control-points-table/26673 "2022-12-12T18:32:48Z")

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I cannot seem to adjust the width of the description field. Name field can be modified but not the description. I would be good to bring back the old behavior This is on windows 11 with 5.2.1

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## [Head circumference or cranial deformation measures from CT](https://discourse.slicer.org/t/head-circumference-or-cranial-deformation-measures-from-ct/14655)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 23\
**Last updated:** [December 12, 2022, 2:21pm UTC](https://discourse.slicer.org/t/head-circumference-or-cranial-deformation-measures-from-ct/14655 "2022-12-12T14:21:57Z")

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Hi: How can I measure the head circumference or cranial deformation measures using CT and 3D Slicer? Automatic or semi-automatic method.

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## [MONAI - Local Project "Tree" and Configuration - Results](https://discourse.slicer.org/t/monai-local-project-tree-and-configuration-results/26664)

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**Author:** [@dalv.silvermann](https://discourse.slicer.org/u/dalv.silvermann)\
**Replies:** 1\
**Last updated:** [December 12, 2022, 1:37pm UTC](https://discourse.slicer.org/t/monai-local-project-tree-and-configuration-results/26664 "2022-12-12T13:37:44Z")

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Dear colleagues, I have a question about the results of MONAI Label Service which I’m using on my tower-server with Asus Nvidia GeForce RTX 3080 10GiB based on Windows Server 2019 OS. We are testing two project struct…

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## [Get best fit sphere of humeral head](https://discourse.slicer.org/t/get-best-fit-sphere-of-humeral-head/22975)

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**Author:** [@osints](https://discourse.slicer.org/u/osints)\
**Replies:** 10\
**Last updated:** [December 7, 2022, 2:58pm UTC](https://discourse.slicer.org/t/get-best-fit-sphere-of-humeral-head/22975 "2022-12-07T14:58:09Z")

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Hi, I am tyring to makes best fit sphere of humeral head. So i makes 3 land marks and then import above code to python interactor. but there is no sphere and some red text is shown… plase some help… thank you

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## [Problem with Running Bone Texture Module](https://discourse.slicer.org/t/problem-with-running-bone-texture-module/26685)

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**Author:** [@berke](https://discourse.slicer.org/u/berke)\
**Replies:** 1\
**Last updated:** [December 11, 2022, 4:17pm UTC](https://discourse.slicer.org/t/problem-with-running-bone-texture-module/26685 "2022-12-11T16:17:26Z")

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Hi everyone, I cropped a volume from a 0.075 mm voxel size CBCT scan and saved it as a .nrrd file. Then i opened the Bone Texture module and set the parameters according to the recommendation in the tutorial file. I cl…

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## [Lung CT Segmentation](https://discourse.slicer.org/t/lung-ct-segmentation/26677)

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**Author:** [@Paula\_R](https://discourse.slicer.org/u/Paula_R)\
**Replies:** 3\
**Last updated:** [December 11, 2022, 11:45am UTC](https://discourse.slicer.org/t/lung-ct-segmentation/26677 "2022-12-11T11:45:04Z")

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Hello, I’ve watched this video: COVID-19 lung CT segmentation using 3D Slicer - YouTube and, in Resample Scalar Volume, Spacing (2,2,2) and linear interpolation are recommended, and I’d like to know why these are the r…

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## [Export DTI as Ply rotational error](https://discourse.slicer.org/t/export-dti-as-ply-rotational-error/26478)

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**Author:** [@yuanci](https://discourse.slicer.org/u/yuanci)\
**Replies:** 7\
**Last updated:** [December 11, 2022, 4:38am UTC](https://discourse.slicer.org/t/export-dti-as-ply-rotational-error/26478 "2022-12-11T04:38:16Z")

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Hi, I’m still trying to figure out the full capabilities of Slicer, and just recently started using the DMRI extension. I tried to export a tract as PLY using the “Export tractography to PLY (mesh)” tool but every time …

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## [Mac Stable (5.2.1.) reports a crash everytime it is closed](https://discourse.slicer.org/t/mac-stable-5-2-1-reports-a-crash-everytime-it-is-closed/26586)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 16\
**Last updated:** [December 10, 2022, 7:55pm UTC](https://discourse.slicer.org/t/mac-stable-5-2-1-reports-a-crash-everytime-it-is-closed/26586 "2022-12-10T19:55:47Z")

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Not sure what to make of this but, even if I simply close Slicer window (with no data loaded into it), I get this crash report from Mac. Otherwise application appears to be working correctly. --------------------------…

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## [Elastix registration fails: Too many samples map outside moving image buffer](https://discourse.slicer.org/t/elastix-registration-fails-too-many-samples-map-outside-moving-image-buffer/15798)

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**Author:** [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Replies:** 18\
**Last updated:** [December 10, 2022, 12:00am UTC](https://discourse.slicer.org/t/elastix-registration-fails-too-many-samples-map-outside-moving-image-buffer/15798 "2022-12-10T00:00:15Z")

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Dear Andras @lassoan . I’m segmenting temporal bone using ABL Temporal Bone Segmentation. I stuck at step 2: Rigid registration. When I apply Rigid registration, the process stopped at 14% and it said: “command ‘elastix…

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## [Loading 3d cine from cardiac MR](https://discourse.slicer.org/t/loading-3d-cine-from-cardiac-mr/26665)

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**Author:** [@RGhosh](https://discourse.slicer.org/u/RGhosh)\
**Replies:** 2\
**Last updated:** [December 9, 2022, 7:14pm UTC](https://discourse.slicer.org/t/loading-3d-cine-from-cardiac-mr/26665 "2022-12-09T19:14:09Z")

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I am having trouble loading a 3d cine from cardiac MR, specifically one obtained using a Phillips scanner. Despite choosing “volume sequence” in Edit–\>settings–\>DICOM, it does not load properly. Instead of each “instance…

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## [Segment Geometry Transformation using python interactor](https://discourse.slicer.org/t/segment-geometry-transformation-using-python-interactor/26162)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 3\
**Last updated:** [December 9, 2022, 2:45pm UTC](https://discourse.slicer.org/t/segment-geometry-transformation-using-python-interactor/26162 "2022-12-09T14:45:07Z")

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Hello~! I was trying to use Segment Geometry using python interactor. I figure out how to get the statistic data but could not make the transformation to work. I tried below script and got following error message. im…

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## [SegmentGeometry](https://discourse.slicer.org/t/segmentgeometry/26661)

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**Author:** [@francesca\_flore](https://discourse.slicer.org/u/francesca_flore)\
**Replies:** 1\
**Last updated:** [December 9, 2022, 1:17pm UTC](https://discourse.slicer.org/t/segmentgeometry/26661 "2022-12-09T13:17:12Z")

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Hi! I’m using SegmentGeometry tool to export a table with the maximum diameter of my segment along its section. But despite I’m computing on every slice in the segment. Not all the slices in which my segment appears are …

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## [Focus 3D view shortcut](https://discourse.slicer.org/t/focus-3d-view-shortcut/26381)

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**Author:** [@Atsui\_75](https://discourse.slicer.org/u/Atsui_75)\
**Replies:** 2\
**Last updated:** [December 9, 2022, 9:30am UTC](https://discourse.slicer.org/t/focus-3d-view-shortcut/26381 "2022-12-09T09:30:43Z")

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Hi: In version 4.11.20210226 when I used to press “F” while placing the mouse cursor on top of a model in the 3D view, the camera got centered where I pressed the button. Is there any way to set up a keyboard shortcut …

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## [Landmark registration morphing ? rigid registration as preprocessing?](https://discourse.slicer.org/t/landmark-registration-morphing-rigid-registration-as-preprocessing/26621)

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**Author:** [@Nicolas\_Tempier](https://discourse.slicer.org/u/Nicolas_Tempier)\
**Replies:** 3\
**Last updated:** [December 9, 2022, 7:24am UTC](https://discourse.slicer.org/t/landmark-registration-morphing-rigid-registration-as-preprocessing/26621 "2022-12-09T07:24:55Z")

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Hi ! i want to registrate a 2D “really high resolution” (29000x26000) as floating image to a “normal” reference image (600x900) Knowing that the high resolution floating image is the same image as the reference one but…

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## [How to use python programming to open and save data in batches?](https://discourse.slicer.org/t/how-to-use-python-programming-to-open-and-save-data-in-batches/26604)

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**Author:** [@lyh-ecnu](https://discourse.slicer.org/u/lyh-ecnu)\
**Replies:** 4\
**Last updated:** [December 9, 2022, 6:54am UTC](https://discourse.slicer.org/t/how-to-use-python-programming-to-open-and-save-data-in-batches/26604 "2022-12-09T06:54:49Z")

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I tried to write a program to open the folder and read several cases inside，but after I run it, only the data of the first case can be successfully loaded, and the following cases will report errors。My code and error mes…

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## [Chest Imaging Platform - Lung Lesion Analyzer error](https://discourse.slicer.org/t/chest-imaging-platform-lung-lesion-analyzer-error/19232)

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**Author:** [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Replies:** 9\
**Last updated:** [December 8, 2022, 6:07pm UTC](https://discourse.slicer.org/t/chest-imaging-platform-lung-lesion-analyzer-error/19232 "2022-12-08T18:07:35Z")

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Hi all, I have run into an issue trying to the Lung Lesion Analyzer submodule from the Chest Imaging Platform extension. For context, this error arises on the current stable build of Slicer on MacOS (version 4.11.202102…

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