# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=147

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

**Page:** 148

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## [Markup gui control via script](https://discourse.slicer.org/t/markup-gui-control-via-script/31041)

<div class="topic-metadata">

**Author:** [@Ylim](https://discourse.slicer.org/u/Ylim)\
**Replies:** 1\
**Last updated:** [August 9, 2023, 5:41pm UTC](https://discourse.slicer.org/t/markup-gui-control-via-script/31041 "2023-08-09T17:41:26Z")

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Hi, Would like to be able script the (a)options to snap at stl, (b) enable length measurement and (c) resample (with defined no. of points) via the markup module? please advise.

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## [How to convert FRM or CSV files to FCSV or JSON format](https://discourse.slicer.org/t/how-to-convert-frm-or-csv-files-to-fcsv-or-json-format/31067)

<div class="topic-metadata">

**Author:** [@AriD](https://discourse.slicer.org/u/AriD)\
**Replies:** 1\
**Last updated:** [August 9, 2023, 4:42pm UTC](https://discourse.slicer.org/t/how-to-convert-frm-or-csv-files-to-fcsv-or-json-format/31067 "2023-08-09T16:42:14Z")

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Hello, I have a CSV file that includes numerous specimens, each with multiple landmark coordinates. Additionally, there are several FRM files for each specimen, also containing various landmark coordinates. Is there…

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## [Smoothing algorithm ](https://discourse.slicer.org/t/smoothing-algorithm/31060)

<div class="topic-metadata">

**Author:** [@Alessia1](https://discourse.slicer.org/u/Alessia1)\
**Replies:** 3\
**Last updated:** [August 9, 2023, 4:37pm UTC](https://discourse.slicer.org/t/smoothing-algorithm/31060 "2023-08-09T16:37:13Z")

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I would like to know which smoothing algorithm is used in Total Segmentator. It would be very helpful in my thesis study. Thanks in advance.

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## [Convert mesh to volume](https://discourse.slicer.org/t/convert-mesh-to-volume/21686)

<div class="topic-metadata">

**Author:** [@Artur\_V](https://discourse.slicer.org/u/Artur_V)\
**Replies:** 5\
**Last updated:** [August 9, 2023, 3:16pm UTC](https://discourse.slicer.org/t/convert-mesh-to-volume/21686 "2023-08-09T15:16:50Z")

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Thank you for this information, but i ran into some problems with the code and the model is not displayed. I’m trying to convert a .VTK file from an atlas (unstructured grid) into a mesh or volume to create a .nrrd or n…

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## [SEEG plugin software or extension](https://discourse.slicer.org/t/seeg-plugin-software-or-extension/31063)

<div class="topic-metadata">

**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 0\
**Last updated:** [August 9, 2023, 1:28pm UTC](https://discourse.slicer.org/t/seeg-plugin-software-or-extension/31063 "2023-08-09T13:28:47Z")

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Which is an SEEG open source software or 3D Slicer extension? Gonzalo Rojas Costa

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## [Mri brain 3d model](https://discourse.slicer.org/t/mri-brain-3d-model/31061)

<div class="topic-metadata">

**Author:** [@dr\_usman\_sani](https://discourse.slicer.org/u/dr_usman_sani)\
**Replies:** 0\
**Last updated:** [August 9, 2023, 11:29am UTC](https://discourse.slicer.org/t/mri-brain-3d-model/31061 "2023-08-09T11:29:22Z")

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How to select images from mri data? I chose T1w coronal sagittal and axials views of brain but only one of the is in good resolution rest is just like leggo ? How to correct it? Thanks. I need to understand how to correc…

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## [What is the best extension for segmentation of bone?](https://discourse.slicer.org/t/what-is-the-best-extension-for-segmentation-of-bone/31022)

<div class="topic-metadata">

**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 2\
**Last updated:** [August 7, 2023, 12:39pm UTC](https://discourse.slicer.org/t/what-is-the-best-extension-for-segmentation-of-bone/31022 "2023-08-07T12:39:31Z")

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What is the best extension for segmentation of bone for trauma and orthopedic surgeons ? The extenson should segment and solidify bone from CT, and f.e. divide structures like acetabulum and femor head or the carpal bon…

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## [How can I use slicer and virtual reality to guide needle based surgery?](https://discourse.slicer.org/t/how-can-i-use-slicer-and-virtual-reality-to-guide-needle-based-surgery/30964)

<div class="topic-metadata">

**Author:** [@HongtaoZhang](https://discourse.slicer.org/u/HongtaoZhang)\
**Replies:** 2\
**Last updated:** [August 9, 2023, 6:03am UTC](https://discourse.slicer.org/t/how-can-i-use-slicer-and-virtual-reality-to-guide-needle-based-surgery/30964 "2023-08-09T06:03:37Z")

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I want to use VR to guide needles that puncture into tumors.

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## [Model Registration - Thin plate spline / B-spline](https://discourse.slicer.org/t/model-registration-thin-plate-spline-b-spline/31050)

<div class="topic-metadata">

**Author:** [@Vignesh\_Chakravarthy](https://discourse.slicer.org/u/Vignesh_Chakravarthy)\
**Replies:** 0\
**Last updated:** [August 8, 2023, 7:24pm UTC](https://discourse.slicer.org/t/model-registration-thin-plate-spline-b-spline/31050 "2023-08-08T19:24:33Z")

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I am using Slicer 5.2.2. Please let me there is a module/option available to do TPS/ B-spline transform on models created. I can do linear transform using the module - “model registration”. However, I also need to apply …

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## [Issue Importing DICOM with overview image](https://discourse.slicer.org/t/issue-importing-dicom-with-overview-image/30933)

<div class="topic-metadata">

**Author:** [@gendex](https://discourse.slicer.org/u/gendex)\
**Replies:** 9\
**Last updated:** [August 8, 2023, 5:05pm UTC](https://discourse.slicer.org/t/issue-importing-dicom-with-overview-image/30933 "2023-08-08T17:05:36Z")

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We just started using Slicer and ran into the following issues: Slicer 4.10.2 Tests -loaded image stack without overview image (both with and without “apply regularization transform”) -get error: Irregular volume geom…

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## [Unity tracking bridge client and ultrasound server... help needed](https://discourse.slicer.org/t/unity-tracking-bridge-client-and-ultrasound-server-help-needed/26324)

<div class="topic-metadata">

**Author:** [@Allan](https://discourse.slicer.org/u/Allan)\
**Replies:** 3\
**Last updated:** [August 8, 2023, 4:47pm UTC](https://discourse.slicer.org/t/unity-tracking-bridge-client-and-ultrasound-server-help-needed/26324 "2023-08-08T16:47:25Z")

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Hi all, I am pretty new to slicer, actually I stumbled over it yesterday and I have a problem that could be easy to solve or it is just impossible :slight\_smile: I have some experience in spatial tracking using unity w…

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## [Extension manager](https://discourse.slicer.org/t/extension-manager/31040)

<div class="topic-metadata">

**Author:** [@Kening\_Zhang](https://discourse.slicer.org/u/Kening_Zhang)\
**Replies:** 3\
**Last updated:** [August 8, 2023, 3:07pm UTC](https://discourse.slicer.org/t/extension-manager/31040 "2023-08-08T15:07:45Z")

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Dear developers， I want to upload the extension created by myself, ExtensionsIndex/.github/PULL\_REQUEST\_TEMPLATE.md at main · Slicer/ExtensionsIndex · GitHub Is this the tutorial about how to making it? Best wishes, …

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## [Unable to import Brainlab SEG to Slicer](https://discourse.slicer.org/t/unable-to-import-brainlab-seg-to-slicer/30684)

<div class="topic-metadata">

**Author:** [@Michele\_Bailo](https://discourse.slicer.org/u/Michele_Bailo)\
**Replies:** 8\
**Last updated:** [August 8, 2023, 1:30pm UTC](https://discourse.slicer.org/t/unable-to-import-brainlab-seg-to-slicer/30684 "2023-08-08T13:30:14Z")

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Hi everyone, I regularly export Slicer segmentations into the Brainlab Elements and Neuronavigation system (using the QuantitativeReporting feature). However, I’ve been experiencing many difficulties in importing segmen…

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## [improper 3D rendering](https://discourse.slicer.org/t/improper-3d-rendering/31044)

<div class="topic-metadata">

**Author:** [@Aakash\_Raval](https://discourse.slicer.org/u/Aakash_Raval)\
**Replies:** 1\
**Last updated:** [August 8, 2023, 1:25pm UTC](https://discourse.slicer.org/t/improper-3d-rendering/31044 "2023-08-08T13:25:47Z")

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I have segmented full skull but in 3D it is cutting the surface is there any solution for this behavior.

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## [How to extract RT dose feature](https://discourse.slicer.org/t/how-to-extract-rt-dose-feature/30842)

<div class="topic-metadata">

**Author:** [@zhuyingying1234](https://discourse.slicer.org/u/zhuyingying1234)\
**Replies:** 1\
**Last updated:** [July 28, 2023, 4:34pm UTC](https://discourse.slicer.org/t/how-to-extract-rt-dose-feature/30842 "2023-07-28T16:34:51Z")

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Dear Slicer experts, I have export RT dose RT plan and RT structures to 3D slicer, how to extract RT dose feature? similar to extract CT image feature ? Am I right ? Many thanks in advance for your advice! Regard…

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## [Airway segmentation can not select dicom volume](https://discourse.slicer.org/t/airway-segmentation-can-not-select-dicom-volume/31016)

<div class="topic-metadata">

**Author:** [@MikhayEeer](https://discourse.slicer.org/u/MikhayEeer)\
**Replies:** 2\
**Last updated:** [August 8, 2023, 4:36am UTC](https://discourse.slicer.org/t/airway-segmentation-can-not-select-dicom-volume/31016 "2023-08-08T04:36:12Z")

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I am a new slicer user. I have already loaded Dicom data , and I can edit the dicom volume in Editor Effect.But I found that if I try to use Extensions like Airway Segmentation or LungCT Segmenter, the CT volume selector…

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## [Seperation plane following closed curve](https://discourse.slicer.org/t/seperation-plane-following-closed-curve/30995)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 4\
**Last updated:** [August 7, 2023, 5:11pm UTC](https://discourse.slicer.org/t/seperation-plane-following-closed-curve/30995 "2023-08-07T17:11:39Z")

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I often work with complicated osteotomy geometry that doesn’t follow straight lines or curves. I need to experiment with many shapes to see the outcome. it would be so good if I could draw a closed curve and a plane is…

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## [Failed to load nifti file](https://discourse.slicer.org/t/failed-to-load-nifti-file/31023)

<div class="topic-metadata">

**Author:** [@Zeynep\_Erdogan](https://discourse.slicer.org/u/Zeynep_Erdogan)\
**Replies:** 0\
**Last updated:** [August 7, 2023, 9:52am UTC](https://discourse.slicer.org/t/failed-to-load-nifti-file/31023 "2023-08-07T09:52:10Z")

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Hi Mr. Lasso, I am trying to import some NIFTI files from the total segmentator dataset in Slicer 5.2.2. But some files are not open and give an error like this:“\[VTK\] ReadData: This is not a nrrd file \[VTK\] vtkMRMLStor…

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## [Is there any code to control 'specify geometry in Segment editor?](https://discourse.slicer.org/t/is-there-any-code-to-control-specify-geometry-in-segment-editor/31021)

<div class="topic-metadata">

**Author:** [@telomere](https://discourse.slicer.org/u/telomere)\
**Replies:** 1\
**Last updated:** [August 7, 2023, 9:07am UTC](https://discourse.slicer.org/t/is-there-any-code-to-control-specify-geometry-in-segment-editor/31021 "2023-08-07T09:07:20Z")

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I made a shortcut to go Segment Editor module and automatically load source volume and add segmentation and segment. In this situation, I also want to control “specify geometry” button which is next to source volume. I…

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## [How to select a volume automatically in volume rendering?](https://discourse.slicer.org/t/how-to-select-a-volume-automatically-in-volume-rendering/30989)

<div class="topic-metadata">

**Author:** [@telomere](https://discourse.slicer.org/u/telomere)\
**Replies:** 4\
**Last updated:** [August 7, 2023, 8:09am UTC](https://discourse.slicer.org/t/how-to-select-a-volume-automatically-in-volume-rendering/30989 "2023-08-07T08:09:43Z")

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Hi, I’m making some script to make my work faster. I made a simple shortcut button that just goes to volume rendering. When it changes to volume rendering module, no volume is selected as a default(even when some volum…

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## [General Registration (Elastix) for two CT-Volumes with differing Voxel Size](https://discourse.slicer.org/t/general-registration-elastix-for-two-ct-volumes-with-differing-voxel-size/30993)

<div class="topic-metadata">

**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 1\
**Last updated:** [August 6, 2023, 11:42pm UTC](https://discourse.slicer.org/t/general-registration-elastix-for-two-ct-volumes-with-differing-voxel-size/30993 "2023-08-06T23:42:03Z")

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Dear Community, my goal is to automatically align two CT-Volumes that have different voxel sizes. I concluded it is best to use the General Registration (Elastix) module. By creating an Output transform and applying it …

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## [Issues when using Binary Image Erode Filter](https://discourse.slicer.org/t/issues-when-using-binary-image-erode-filter/31009)

<div class="topic-metadata">

**Author:** [@Annabel\_W](https://discourse.slicer.org/u/Annabel_W)\
**Replies:** 1\
**Last updated:** [August 6, 2023, 6:23pm UTC](https://discourse.slicer.org/t/issues-when-using-binary-image-erode-filter/31009 "2023-08-06T18:23:28Z")

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Hi There, I am working on a project that will allow me to automate the localization of intracranial electrodes using Pre and Post Surgical CTs and a Pre Surgical MRI on 3D Slicer. I am Currently trying to remove the ou…

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## [Virus threat protection](https://discourse.slicer.org/t/virus-threat-protection/31005)

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**Author:** [@vrancois](https://discourse.slicer.org/u/vrancois)\
**Replies:** 3\
**Last updated:** [August 6, 2023, 9:16am UTC](https://discourse.slicer.org/t/virus-threat-protection/31005 "2023-08-06T09:16:48Z")

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Operating system:wINDOWS10 Slicer version:5.2.2 Won’t access database folder on my work computer because windows detected Slicer as a threat Any ideas how I can fix this?

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## [Optimizing resolution and spacing parameters in Plastimatch DRR](https://discourse.slicer.org/t/optimizing-resolution-and-spacing-parameters-in-plastimatch-drr/25873)

<div class="topic-metadata">

**Author:** [@fieldr4](https://discourse.slicer.org/u/fieldr4)\
**Replies:** 65\
**Last updated:** [August 5, 2023, 6:44pm UTC](https://discourse.slicer.org/t/optimizing-resolution-and-spacing-parameters-in-plastimatch-drr/25873 "2023-08-05T18:44:32Z")

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Hi, I am using Plastimatch DRR module within the SlicerRT extension to create synthetic lateral x-rays from a CT volume. I am trying to produce DRRs with the clearest vertebral margins (minimizing blur due to pixelation…

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## [Segmentation overlay](https://discourse.slicer.org/t/segmentation-overlay/30985)

<div class="topic-metadata">

**Author:** [@Alra2000](https://discourse.slicer.org/u/Alra2000)\
**Replies:** 2\
**Last updated:** [August 5, 2023, 3:37pm UTC](https://discourse.slicer.org/t/segmentation-overlay/30985 "2023-08-05T15:37:27Z")

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Hello everyone, I am segmenting laser ablation tissue on brain MRI, and I am trying to overlay the segmentations for volume comparison. Is there an option for that in 3D slicer, please?

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## [Capturing a Screenshot in uncompressed TIFF format](https://discourse.slicer.org/t/capturing-a-screenshot-in-uncompressed-tiff-format/30991)

<div class="topic-metadata">

**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 2\
**Last updated:** [August 5, 2023, 11:09am UTC](https://discourse.slicer.org/t/capturing-a-screenshot-in-uncompressed-tiff-format/30991 "2023-08-05T11:09:39Z")

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Hello dear Comunity, when capturing a screenshot of the multiplanar view of a CBCT volume, the only option Slicer gives me is to save it in png. format. The resolution of the saved image is inferior to the one of the CB…

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## [How to auto export Segmentation-Labels.tiff and Original images from .mrb file?](https://discourse.slicer.org/t/how-to-auto-export-segmentation-labels-tiff-and-original-images-from-mrb-file/30986)

<div class="topic-metadata">

**Author:** [@Jeff\_Boker](https://discourse.slicer.org/u/Jeff_Boker)\
**Replies:** 1\
**Last updated:** [August 5, 2023, 10:35am UTC](https://discourse.slicer.org/t/how-to-auto-export-segmentation-labels-tiff-and-original-images-from-mrb-file/30986 "2023-08-05T10:35:04Z")

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I have several .mrb files which contain images and segmentation annotations. I currently manually open the .mrb file in 3D slicer and then go to “Data” → “Export visible segments to binary labelmap” → “Save” and then sel…

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## [3D+t - Longitudinal Volume Comparison - is there an option?](https://discourse.slicer.org/t/3d-t-longitudinal-volume-comparison-is-there-an-option/30981)

<div class="topic-metadata">

**Author:** [@SlicerDicer](https://discourse.slicer.org/u/SlicerDicer)\
**Replies:** 2\
**Last updated:** [August 5, 2023, 10:31am UTC](https://discourse.slicer.org/t/3d-t-longitudinal-volume-comparison-is-there-an-option/30981 "2023-08-05T10:31:19Z")

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Hello everyone, thank you very much for your time, I have been enjoying Slicer and its features very much. Similarly to Linking\_Views, I have been using the CompareVolume Feature for registered images, and it is very h…

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## [Mandible jawbone geometry and bone specification  ](https://discourse.slicer.org/t/mandible-jawbone-geometry-and-bone-specification/30982)

<div class="topic-metadata">

**Author:** [@Talei\_Al-Matrafi](https://discourse.slicer.org/u/Talei_Al-Matrafi)\
**Replies:** 0\
**Last updated:** [August 4, 2023, 5:57pm UTC](https://discourse.slicer.org/t/mandible-jawbone-geometry-and-bone-specification/30982 "2023-08-04T17:57:05Z")

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Hi i am a phd student , i want to get the 3D model for a mandible jawbone with a full information of bone specification (geometry measurement , the bone specification like the cortical and cancellous bone thickness and…

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## [Level Tracing and Reformatting the View](https://discourse.slicer.org/t/level-tracing-and-reformatting-the-view/30978)

<div class="topic-metadata">

**Author:** [@Dominick\_Dickerson](https://discourse.slicer.org/u/Dominick_Dickerson)\
**Replies:** 1\
**Last updated:** [August 4, 2023, 3:18pm UTC](https://discourse.slicer.org/t/level-tracing-and-reformatting-the-view/30978 "2023-08-04T15:18:22Z")

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It appears that the level tracing tool only works in the initial axial/saggital/coronal planes and not when the view of the slice is reformatted using the reformat widget. Is this because the “level tracing” tool has th…

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