# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=245

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

**Page:** 246

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## [Otsu segmentation on Head and Neck PET image](https://discourse.slicer.org/t/otsu-segmentation-on-head-and-neck-pet-image/21235)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 1\
**Last updated:** [December 27, 2021, 12:52pm UTC](https://discourse.slicer.org/t/otsu-segmentation-on-head-and-neck-pet-image/21235 "2021-12-27T12:52:15Z")

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Operating system: Windows 11 home Slicer version:Slicer 4.13.0-2021-12-22 Is it advisable to use otsu method to segment tumour (marked in blue) on PET images? If it is possible, please guide me to the relevant resource…

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## [Differences in between volume rendering and gray scale model in Registration](https://discourse.slicer.org/t/differences-in-between-volume-rendering-and-gray-scale-model-in-registration/17720)

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**Author:** [@nayanw775](https://discourse.slicer.org/u/nayanw775)\
**Replies:** 14\
**Last updated:** [December 27, 2021, 12:40pm UTC](https://discourse.slicer.org/t/differences-in-between-volume-rendering-and-gray-scale-model-in-registration/17720 "2021-12-27T12:40:23Z")

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Operating system: Windows 10 Slicer version:4.11 Hello Slicer community, I am unable to create accurate grey scale model so that its quality matches up to the standards of Volume rendering at the point of registration…

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## [Applying various segmentation method on same PET/CT image](https://discourse.slicer.org/t/applying-various-segmentation-method-on-same-pet-ct-image/20851)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 7\
**Last updated:** [December 9, 2021, 10:40am UTC](https://discourse.slicer.org/t/applying-various-segmentation-method-on-same-pet-ct-image/20851 "2021-12-09T10:40:26Z")

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Operating system:Windows 10 enterprise Slicer version:Slicer 4.13.0-2021-10-25 Hi, I would like to know whether it is possible to apply various semi-automated segmentation methods on the same loaded PET-CT image by hi…

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## [Different semi-automatic segmentation method on PET image](https://discourse.slicer.org/t/different-semi-automatic-segmentation-method-on-pet-image/21236)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 0\
**Last updated:** [December 27, 2021, 12:35pm UTC](https://discourse.slicer.org/t/different-semi-automatic-segmentation-method-on-pet-image/21236 "2021-12-27T12:35:11Z")

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Operating system: Windows 11 home Slicer version: Slicer 4.13.0-2021-12-15 Hi, I have a few questions relating to applying different segmentation method on a PET image. I have applied a few segmentation methods on m…

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## [combine a 3d dental scan with a DICOM  file ](https://discourse.slicer.org/t/combine-a-3d-dental-scan-with-a-dicom-file/21226)

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**Author:** [@seni4it](https://discourse.slicer.org/u/seni4it)\
**Replies:** 0\
**Last updated:** [December 27, 2021, 2:02am UTC](https://discourse.slicer.org/t/combine-a-3d-dental-scan-with-a-dicom-file/21226 "2021-12-27T02:02:02Z")

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hay everybody i wold like to create surgical guides in dentistry the problem is that the patient have crowns and there are a lot of artifacts, so i cannot create a precise STL file or slice the teeth correctly. i can d…

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## [ShapeQuantifier module is not loaded](https://discourse.slicer.org/t/shapequantifier-module-is-not-loaded/21212)

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**Author:** [@yasser](https://discourse.slicer.org/u/yasser)\
**Replies:** 0\
**Last updated:** [December 26, 2021, 6:10am UTC](https://discourse.slicer.org/t/shapequantifier-module-is-not-loaded/21212 "2021-12-26T06:10:30Z")

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hello everyone, I am new to using 3D slicer and everything is going fine so far except when I try to use Shape Quantifier it gives me a message in red stating its not loaded even though I downloaded it can anyone pleas…

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## [Slow 2d slice update speed](https://discourse.slicer.org/t/slow-2d-slice-update-speed/21206)

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**Author:** [@Hitesh\_Ganjoo](https://discourse.slicer.org/u/Hitesh_Ganjoo)\
**Replies:** 0\
**Last updated:** [December 25, 2021, 7:48pm UTC](https://discourse.slicer.org/t/slow-2d-slice-update-speed/21206 "2021-12-25T19:48:51Z")

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Hi, I am trying to update the 2D slice views based on a normal(using the plane perpendicular to the normal as the slice plane). I am facing an issue with fast update of 2D views, and on initial analysis, it seems like …

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## [Model to model distance filter - completed with error!](https://discourse.slicer.org/t/model-to-model-distance-filter-completed-with-error/21124)

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**Author:** [@MAXFAXSURGEON](https://discourse.slicer.org/u/MAXFAXSURGEON)\
**Replies:** 3\
**Last updated:** [December 25, 2021, 3:09am UTC](https://discourse.slicer.org/t/model-to-model-distance-filter-completed-with-error/21124 "2021-12-25T03:09:01Z")

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PLEASE COULD ANY ONE HELP ME FIGURE OUT WHY THIS IS KEEP HAPPENING WITH ME, IT IS REALLY DRIVING ME CREAZY! FIND ATTACHED THE DEBUG REPORT AND THE MODEL SAMPLE I HAVE WORKED ON. https://drive.google.com/drive/folders/1…

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## [RT phantom drawing](https://discourse.slicer.org/t/rt-phantom-drawing/21189)

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**Author:** [@naninano1](https://discourse.slicer.org/u/naninano1)\
**Replies:** 3\
**Last updated:** [December 24, 2021, 8:45pm UTC](https://discourse.slicer.org/t/rt-phantom-drawing/21189 "2021-12-24T20:45:09Z")

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Hello, I want to draw a patient phantom with regular shapes (ellipse, sphere, cube, etc) as body, organs at risk, tumor, etc. as CT Dicom images, but I am not sure whether it is possible with Slicer 3d or not. I have s…

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## [Segmentation visualization toggle is linked when it should not](https://discourse.slicer.org/t/segmentation-visualization-toggle-is-linked-when-it-should-not/19940)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 19\
**Last updated:** [December 24, 2021, 4:49pm UTC](https://discourse.slicer.org/t/segmentation-visualization-toggle-is-linked-when-it-should-not/19940 "2021-12-24T16:49:41Z")

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It appears that toggling visibility of segmentation in slice view toggles all of the viewers, even if the views are unlinked. Is this a bug? I see the same behavior both in latest and stable. If I export segmentation as …

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## [Segmentation creation](https://discourse.slicer.org/t/segmentation-creation/21184)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 1\
**Last updated:** [December 23, 2021, 4:02pm UTC](https://discourse.slicer.org/t/segmentation-creation/21184 "2021-12-23T16:02:27Z")

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Hi everyone, I have to segment the MRBrain considering white matter, gray matter, CFS, skull etc. How can I create an mhd file consisting of some of these objects? (e.g. how can I get one file / segment which contains o…

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## [Segmentation saving support](https://discourse.slicer.org/t/segmentation-saving-support/21183)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 1\
**Last updated:** [December 23, 2021, 4:01pm UTC](https://discourse.slicer.org/t/segmentation-saving-support/21183 "2021-12-23T16:01:46Z")

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Hi everyone, I did a segmentation of a brain with a tumor (specifically the MRBrainTumor2 in BuiltIn). I’m having trouble with the save operation. How can I get 2 different mhd files for the two objects? In the save lis…

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## [Sequence Registration for 4D CT](https://discourse.slicer.org/t/sequence-registration-for-4d-ct/21180)

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**Author:** [@Cody\_Xie](https://discourse.slicer.org/u/Cody_Xie)\
**Replies:** 2\
**Last updated:** [December 22, 2021, 6:47pm UTC](https://discourse.slicer.org/t/sequence-registration-for-4d-ct/21180 "2021-12-22T18:47:52Z")

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Dear all, I have a 4D CT data set which has 8 phases, and I would like to segment the Left Ventricle for all 8 phases automatically (segment phase 0 manually, then the other 7 phases automatically). I followed the guida…

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## [Slicer crashes when I try to record 2 videos at the same time](https://discourse.slicer.org/t/slicer-crashes-when-i-try-to-record-2-videos-at-the-same-time/21176)

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**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 1\
**Last updated:** [December 22, 2021, 2:46pm UTC](https://discourse.slicer.org/t/slicer-crashes-when-i-try-to-record-2-videos-at-the-same-time/21176 "2021-12-22T14:46:00Z")

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Hi, I am trying to record 2 videos at the same time using the python APIs. If I record just one video, the recording works properly, but if I immediatelly start a second recording Slicer crashes. However if I wait som…

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## [Nvidia AIAA clara\_pt\_covid19\_ct\_lung\_segmentation model doesn't show up](https://discourse.slicer.org/t/nvidia-aiaa-clara-pt-covid19-ct-lung-segmentation-model-doesnt-show-up/21177)

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**Author:** [@utkgl](https://discourse.slicer.org/u/utkgl)\
**Replies:** 1\
**Last updated:** [December 22, 2021, 1:55pm UTC](https://discourse.slicer.org/t/nvidia-aiaa-clara-pt-covid19-ct-lung-segmentation-model-doesnt-show-up/21177 "2021-12-22T13:55:57Z")

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Hi everyone, Lately I was using Nvidia AIAA module ( clara\_pt\_covid19\_ct\_lung\_segmentation) on 3D Slicer to automatically segmentate and export lungs. On my main computer (with gpu rtx2060) the model shows up but on…

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## [Markups : new point ID restart from 1 when loaded from saved scene](https://discourse.slicer.org/t/markups-new-point-id-restart-from-1-when-loaded-from-saved-scene/21142)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [December 22, 2021, 4:23am UTC](https://discourse.slicer.org/t/markups-new-point-id-restart-from-1-when-loaded-from-saved-scene/21142 "2021-12-22T04:23:23Z")

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I’ve noticed an ID numbering problem with curve and fiducial markups. I have not tested all markups objects. Using home built Slicer on Linux. Found with factory build 4.13.0-2021-11-01 r30345 / 08aeb16 also. Start Sli…

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## [Surface mesh with multiple scalar data](https://discourse.slicer.org/t/surface-mesh-with-multiple-scalar-data/20868)

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**Author:** [@gerroba](https://discourse.slicer.org/u/gerroba)\
**Replies:** 4\
**Last updated:** [December 21, 2021, 2:47pm UTC](https://discourse.slicer.org/t/surface-mesh-with-multiple-scalar-data/20868 "2021-12-21T14:47:59Z")

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Hello Slicer community, I am trying to load a Polydata vtk file that I created using Matlab that contains a surface mesh with multiple scalar variables associated. I am able to load the file (test1.vtk) in Paraview and …

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## [Replay recorded data as a sequence in the SequenceBrowser](https://discourse.slicer.org/t/replay-recorded-data-as-a-sequence-in-the-sequencebrowser/21149)

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**Author:** [@lb123](https://discourse.slicer.org/u/lb123)\
**Replies:** 1\
**Last updated:** [December 21, 2021, 5:28am UTC](https://discourse.slicer.org/t/replay-recorded-data-as-a-sequence-in-the-sequencebrowser/21149 "2021-12-21T05:28:10Z")

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Hi, I recorded a tracked video using the Plus Remote module from Slicer IGT. The recording had been stored as a .igs.mha file. I can replay the recording using Plus Toolkit and the video and the tracking data is visibl…

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## [Fix size in cropped volume](https://discourse.slicer.org/t/fix-size-in-cropped-volume/21114)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 7\
**Last updated:** [December 20, 2021, 9:37pm UTC](https://discourse.slicer.org/t/fix-size-in-cropped-volume/21114 "2021-12-20T21:37:49Z")

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Hi, I want to crop a volume with a fixed size, let’s say 400x400. As far as I know, there is no way to set the dimension of the AnnotationROI in Crop Volume module. (I can do it manually but it’s quite frustrating). Is…

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## [GetNthControlPointOrientationMatrix : How should we consider it?](https://discourse.slicer.org/t/getnthcontrolpointorientationmatrix-how-should-we-consider-it/21131)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 10\
**Last updated:** [December 20, 2021, 7:38am UTC](https://discourse.slicer.org/t/getnthcontrolpointorientationmatrix-how-should-we-consider-it/21131 "2021-12-20T07:38:21Z")

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A markups fiducial node has this function : GetNthControlPointOrientationMatrix. While tinkering with it, it does not get modified if a transform is applied to the fiducial node, nor if it is placed in a reformatted sli…

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## [Resources/Guidance to incorporate tensorflow model to slicer scripted module](https://discourse.slicer.org/t/resources-guidance-to-incorporate-tensorflow-model-to-slicer-scripted-module/20897)

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**Author:** [@Ganeshaaraj](https://discourse.slicer.org/u/Ganeshaaraj)\
**Replies:** 1\
**Last updated:** [December 3, 2021, 2:12pm UTC](https://discourse.slicer.org/t/resources-guidance-to-incorporate-tensorflow-model-to-slicer-scripted-module/20897 "2021-12-03T14:12:06Z")

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Hello, I developed a semantic segmentation model using U-Net (Deep learning architecture) in Tensorflow. Model is fully trained. I want to develop a scripted module in which I want to import that particular model to car…

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## [Cardiac CT left ventricle segmentation](https://discourse.slicer.org/t/cardiac-ct-left-ventricle-segmentation/21121)

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**Author:** [@Francesca\_Lo\_Iacono](https://discourse.slicer.org/u/Francesca_Lo_Iacono)\
**Replies:** 2\
**Last updated:** [December 18, 2021, 1:27am UTC](https://discourse.slicer.org/t/cardiac-ct-left-ventricle-segmentation/21121 "2021-12-18T01:27:33Z")

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Hi guys! I have cardiac CT images and I’m trying to segment the left ventricle cavity and left ventricle wall. I have the edges of them differently colored (green for LV wall and yellow for LV cavity) and I need to …

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## [ModeltoModel Distance module is not working properly!](https://discourse.slicer.org/t/modeltomodel-distance-module-is-not-working-properly/20907)

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**Author:** [@MAXFAXSURGEON](https://discourse.slicer.org/u/MAXFAXSURGEON)\
**Replies:** 17\
**Last updated:** [December 17, 2021, 10:18pm UTC](https://discourse.slicer.org/t/modeltomodel-distance-module-is-not-working-properly/20907 "2021-12-17T22:18:59Z")

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hi , when I am working on Slicer using Pik’n paint and when do Model to Model distance function; suddenly the process ends and (completed with error) appears in the status “as shown in the attached screenshot”, what coul…

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## [Clipping 2D slices in an arbitary shape](https://discourse.slicer.org/t/clipping-2d-slices-in-an-arbitary-shape/20970)

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**Author:** [@Hitesh\_Ganjoo](https://discourse.slicer.org/u/Hitesh_Ganjoo)\
**Replies:** 8\
**Last updated:** [December 17, 2021, 6:10pm UTC](https://discourse.slicer.org/t/clipping-2d-slices-in-an-arbitary-shape/20970 "2021-12-17T18:10:20Z")

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Hi, I want to display a part of the slice data(in any slice view) based on an existing geometric constraint or specifically the 2D projection of a surface model(attaching a sample image). Instead of showing all the voxe…

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## [How to load a .stl segmentation onto a DICOM file with 3D slicer?](https://discourse.slicer.org/t/how-to-load-a-stl-segmentation-onto-a-dicom-file-with-3d-slicer/21111)

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**Author:** [@Callas](https://discourse.slicer.org/u/Callas)\
**Replies:** 1\
**Last updated:** [December 17, 2021, 12:43pm UTC](https://discourse.slicer.org/t/how-to-load-a-stl-segmentation-onto-a-dicom-file-with-3d-slicer/21111 "2021-12-17T12:43:35Z")

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Hello, I am quite new to 3D slicer and I have an issue loading a .stl format segmentation onto a DICOM file. I have the DICOM file (which is a stack of images from a MRI image) and a .stl segmentation. I would like to …

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## [Transform volume with handles](https://discourse.slicer.org/t/transform-volume-with-handles/21112)

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**Author:** [@DNeil](https://discourse.slicer.org/u/DNeil)\
**Replies:** 0\
**Last updated:** [December 17, 2021, 12:24pm UTC](https://discourse.slicer.org/t/transform-volume-with-handles/21112 "2021-12-17T12:24:01Z")

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Hello I use registration of images frequently, using the Brains module. Initially i do a rough align either with the fiducial registion module, or manually visualising the two volumes in the slice view with 50/50 opaci…

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## [Exporting DICOMS with annotations](https://discourse.slicer.org/t/exporting-dicoms-with-annotations/21101)

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**Author:** [@Maharshi\_Panchal](https://discourse.slicer.org/u/Maharshi_Panchal)\
**Replies:** 1\
**Last updated:** [December 17, 2021, 1:20am UTC](https://discourse.slicer.org/t/exporting-dicoms-with-annotations/21101 "2021-12-17T01:20:09Z")

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Hello, I was wondering if there was a way to export DICOM images after making annotations on them. For example, if I mark CT scans slice-by-slice using the “draw” effect in Segment Editor, is there any way for me to exp…

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## [Gap between segments in 3D view](https://discourse.slicer.org/t/gap-between-segments-in-3d-view/21056)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 6\
**Last updated:** [December 16, 2021, 8:13pm UTC](https://discourse.slicer.org/t/gap-between-segments-in-3d-view/21056 "2021-12-16T20:13:52Z")

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I noticed this gap between 2 segments in 3D view, while it does not exist in slice views. Load any volume Create a new segmentation Paint a segment on a single slice Paint a second smaller segment inside the first on…

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## [Post-correct registration](https://discourse.slicer.org/t/post-correct-registration/21097)

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**Author:** [@Francesca\_Pittoni](https://discourse.slicer.org/u/Francesca_Pittoni)\
**Replies:** 0\
**Last updated:** [December 16, 2021, 6:54pm UTC](https://discourse.slicer.org/t/post-correct-registration/21097 "2021-12-16T18:54:22Z")

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Hi everyone, I performed a sequence registration (fixed frame 4, from fixed to moving frame), and as you can see, in some frames it is not so accurate. Since I need an accurate sequence transform (I have to apply it to…

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## [2 Images in Oculus Ques2 and Rift](https://discourse.slicer.org/t/2-images-in-oculus-ques2-and-rift/21066)

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**Author:** [@August\_de\_Oliveira](https://discourse.slicer.org/u/August_de_Oliveira)\
**Replies:** 2\
**Last updated:** [December 16, 2021, 6:26pm UTC](https://discourse.slicer.org/t/2-images-in-oculus-ques2-and-rift/21066 "2021-12-16T18:26:42Z")

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Hello! I tried to use the VR extension of Slicer and I get two images (One per eye). I am running steam VR. I am sure it is just a setting. Thanks in advance for your advice.

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