# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=272

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

**Page:** 273

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## [ConvertToGridTransform returns vtkMRMLTransformNode instead of vtkMRMLGridTransformNode](https://discourse.slicer.org/t/converttogridtransform-returns-vtkmrmltransformnode-instead-of-vtkmrmlgridtransformnode/18467)

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**Author:** [@simonoxen](https://discourse.slicer.org/u/simonoxen)\
**Replies:** 2\
**Last updated:** [July 2, 2021, 6:19am UTC](https://discourse.slicer.org/t/converttogridtransform-returns-vtkmrmltransformnode-instead-of-vtkmrmlgridtransformnode/18467 "2021-07-02T06:19:18Z")

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Is there a reason why the ConvertToGridTransform method outputs a vtkMRMLTransformNode instead of a vtkMRMLGridTransformNode? Slicer/Modules/Loadable/Transforms/Logic/vtkSlicerTransformLogic.h I’m developing a module t…

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## [Edit existing segmentation](https://discourse.slicer.org/t/edit-existing-segmentation/6917)

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**Author:** [@Christineseven](https://discourse.slicer.org/u/Christineseven)\
**Replies:** 8\
**Last updated:** [July 2, 2021, 5:10am UTC](https://discourse.slicer.org/t/edit-existing-segmentation/6917 "2021-07-02T05:10:52Z")

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Hello. I would like to ask, in image segmentation, when we have already the predicted mask and we want to correct it.What is the way to remove parts of the mask or add some parts(painting) to the already masks? without p…

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## [Help with T1 and FLAIR registration](https://discourse.slicer.org/t/help-with-t1-and-flair-registration/18473)

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**Author:** [@J1234](https://discourse.slicer.org/u/J1234)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 5:08am UTC](https://discourse.slicer.org/t/help-with-t1-and-flair-registration/18473 "2021-07-02T05:08:47Z")

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Operating system: Mac OS Slicer version: 4.11.20210226 New 3D Slicer user here. I have a T1 and a FLAIR image that I need to align in space. I’ve conducted “Registration” → Resample Images (BRAINS) and “warped” the FLA…

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## [WSS visualization](https://discourse.slicer.org/t/wss-visualization/18456)

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**Author:** [@CandeMorello](https://discourse.slicer.org/u/CandeMorello)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:25am UTC](https://discourse.slicer.org/t/wss-visualization/18456 "2021-07-02T04:25:52Z")

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Hi everyone good morning. I have performed several CDF simulations and extracted wall shear stress maps on the surfaces of my models. The thing is that I can visualize the WSS maps in paraview. What I want to do is to …

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## [Implementing Slicer rigid registration in ITK](https://discourse.slicer.org/t/implementing-slicer-rigid-registration-in-itk/18441)

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**Author:** [@rz93](https://discourse.slicer.org/u/rz93)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:23am UTC](https://discourse.slicer.org/t/implementing-slicer-rigid-registration-in-itk/18441 "2021-07-02T04:23:56Z")

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I am trying to register two CT head images from the same subjects. There exists significant rotations and one image is significantly cropped than the other. I used the General Registration (BRAINS) rigid registration wi…

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## [How to save brain structural edited masks (segment edited) in nifti for freesurfer use?](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429)

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**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:04am UTC](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429 "2021-07-02T04:04:46Z")

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Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some editing, and I used Slicer Segment Editor for it (opened mask as label \> imported labelmap as segmentation \> …

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## [Creating sub-segments](https://discourse.slicer.org/t/creating-sub-segments/18420)

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**Author:** [@trash\_imp](https://discourse.slicer.org/u/trash_imp)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 3:36am UTC](https://discourse.slicer.org/t/creating-sub-segments/18420 "2021-07-02T03:36:35Z")

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While implementing Grow from seeds, In Slicer3D, we create new Segments when we want to split the dicom, and then we click on implement. I want to modify segments so that the children of a segment(sub-segments) are…

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## [Exporting segmentation problem](https://discourse.slicer.org/t/exporting-segmentation-problem/6813)

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**Author:** [@David\_M](https://discourse.slicer.org/u/David_M)\
**Replies:** 2\
**Last updated:** [July 2, 2021, 3:33am UTC](https://discourse.slicer.org/t/exporting-segmentation-problem/6813 "2021-07-02T03:33:19Z")

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Operating system: windows 7 Slicer version: 4.10.1 Expected behavior: Exporting the segmentation I see on the screen Actual behavior: Exporting extra volume Hi, I would like to report this issue, that I can’t fix. I…

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## [Slicer icons location](https://discourse.slicer.org/t/slicer-icons-location/18458)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 2\
**Last updated:** [July 2, 2021, 2:49am UTC](https://discourse.slicer.org/t/slicer-icons-location/18458 "2021-07-02T02:49:14Z")

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In which directory are all the icons located in Slicer? For example all the markup icons fiducial,ruler etc. icons. I was not able to find them in slicer.

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## [Smoothing with Gaussian standard deviation changed at some point](https://discourse.slicer.org/t/smoothing-with-gaussian-standard-deviation-changed-at-some-point/18431)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 3\
**Last updated:** [July 1, 2021, 1:18pm UTC](https://discourse.slicer.org/t/smoothing-with-gaussian-standard-deviation-changed-at-some-point/18431 "2021-07-01T13:18:03Z")

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I was using the Smoothing segment editor effect recently and noticed a change in results using a typical value for Gaussian standard deviation mm. A commit from Oct 19th, 2020 ( ENH: Add brush option to Segment Editor…

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## [Import DICOM after format change from NETCDF using pydicom](https://discourse.slicer.org/t/import-dicom-after-format-change-from-netcdf-using-pydicom/18312)

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**Author:** [@asims](https://discourse.slicer.org/u/asims)\
**Replies:** 2\
**Last updated:** [July 1, 2021, 1:52am UTC](https://discourse.slicer.org/t/import-dicom-after-format-change-from-netcdf-using-pydicom/18312 "2021-07-01T01:52:43Z")

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OS: Windows 10 64bit Slicer Version:4.10.0 Hi I have a lab CT scan of an item stored in NETCDF (\*.nc) format in multiple blocks. I would like to open this in Slicer. I have converted to dicom slices (1 file per slice)…

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## [Saving image file in .mha format](https://discourse.slicer.org/t/saving-image-file-in-mha-format/11703)

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**Author:** [@YolkandWhite](https://discourse.slicer.org/u/YolkandWhite)\
**Replies:** 3\
**Last updated:** [May 26, 2020, 4:39am UTC](https://discourse.slicer.org/t/saving-image-file-in-mha-format/11703 "2020-05-26T04:39:04Z")

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Hi I have an easy question about .mha file format. I have an original image file in .png format I loaded that file to 3D slicer and saved it in .mha format. and than image size got largen. The original .png file was …

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## [Converting Pathological Results to 3D](https://discourse.slicer.org/t/converting-pathological-results-to-3d/18436)

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**Author:** [@arif](https://discourse.slicer.org/u/arif)\
**Replies:** 1\
**Last updated:** [June 30, 2021, 6:55pm UTC](https://discourse.slicer.org/t/converting-pathological-results-to-3d/18436 "2021-06-30T18:55:45Z")

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Hi dear slicer users; I am trying to convert pathological results to 3D. But my results are not usable. I know that with 8 slices to use, I won’t get any good surface or the best accuracy, but if you have any suggestio…

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## [Split images and corresponding labels in half (symmetric cropping)](https://discourse.slicer.org/t/split-images-and-corresponding-labels-in-half-symmetric-cropping/18435)

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**Author:** [@mluerig](https://discourse.slicer.org/u/mluerig)\
**Replies:** 1\
**Last updated:** [June 30, 2021, 4:16pm UTC](https://discourse.slicer.org/t/split-images-and-corresponding-labels-in-half-symmetric-cropping/18435 "2021-06-30T16:16:18Z")

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I need to split a bunch of images and corresponding labels in half. The images do not have the same dimensions. I tried with the cropping tool, but I can’t get it exactly in half, I don’t know how I would invert the cro…

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## [Possibility to export only subset of labelled slices?](https://discourse.slicer.org/t/possibility-to-export-only-subset-of-labelled-slices/18255)

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**Author:** [@mluerig](https://discourse.slicer.org/u/mluerig)\
**Replies:** 10\
**Last updated:** [June 30, 2021, 3:17pm UTC](https://discourse.slicer.org/t/possibility-to-export-only-subset-of-labelled-slices/18255 "2021-06-30T15:17:37Z")

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I am trying to get started with biomedisa (https://biomedisa.org/), a deep learning based automatic segmentation tool which uses a subset of labels (e.g., only every 10th label from a stack of slices) to segment all rema…

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## [How to use command line run slicer's models](https://discourse.slicer.org/t/how-to-use-command-line-run-slicers-models/18427)

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**Author:** [@lyhsky123](https://discourse.slicer.org/u/lyhsky123)\
**Replies:** 2\
**Last updated:** [June 30, 2021, 1:44pm UTC](https://discourse.slicer.org/t/how-to-use-command-line-run-slicers-models/18427 "2021-06-30T13:44:10Z")

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When I use Mac command line to run this: /Applications/Slicer.app/Contents/MacOS/Slicer --launch ResampleScalarVolume -i linear -s 1,1,1 $CoregPath/Coreg\_$MRI.nii.gz $CoregPath/CoregResamp\_$MRI.nii.gz It always swi…

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## [How to compute oriented bounding box for a model and display it using annotation ROI?](https://discourse.slicer.org/t/how-to-compute-oriented-bounding-box-for-a-model-and-display-it-using-annotation-roi/18411)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 3\
**Last updated:** [June 30, 2021, 3:02am UTC](https://discourse.slicer.org/t/how-to-compute-oriented-bounding-box-for-a-model-and-display-it-using-annotation-roi/18411 "2021-06-30T03:02:58Z")

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In Get size, position, and orientation of each segment, I learned how to compute oriented bounding box for each segment and displays them using annotation ROI. I want to know how to compute oriented bounding box for a m…

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## [Importing PBS files ](https://discourse.slicer.org/t/importing-pbs-files/18401)

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**Author:** [@manuela\_lizarazu](https://discourse.slicer.org/u/manuela_lizarazu)\
**Replies:** 3\
**Last updated:** [June 30, 2021, 2:42am UTC](https://discourse.slicer.org/t/importing-pbs-files/18401 "2021-06-30T02:42:37Z")

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Slicer version: 4.11 Can PSB files be uploaded into slicer? I am working with photoshop and I have 96 images with 4800 pixels each, a really big file (PBS file is the only saving option I have), and I need to import it …

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## [How to do volume rendering with original intensity](https://discourse.slicer.org/t/how-to-do-volume-rendering-with-original-intensity/18333)

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**Author:** [@pranaysingh](https://discourse.slicer.org/u/pranaysingh)\
**Replies:** 3\
**Last updated:** [June 30, 2021, 1:54am UTC](https://discourse.slicer.org/t/how-to-do-volume-rendering-with-original-intensity/18333 "2021-06-30T01:54:28Z")

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Hi, I am trying to do volume rendering of my dicom dataset. I am able to successfully view my 3D object but its black in color. While my object, which is actually a tooth is somewhat gray and white in color, which is ac…

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## [Cross Section Slices Displayed Side-by-Side](https://discourse.slicer.org/t/cross-section-slices-displayed-side-by-side/18379)

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**Author:** [@dsoto](https://discourse.slicer.org/u/dsoto)\
**Replies:** 2\
**Last updated:** [June 29, 2021, 8:17pm UTC](https://discourse.slicer.org/t/cross-section-slices-displayed-side-by-side/18379 "2021-06-29T20:17:47Z")

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I want to determine changes in a very specific area of an MRI over time. Specifically, I want to draw a line through an organ and have it take the same line from all 300 frames in a data set and display them side-by-side…

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## [Fullscreen the 3D view](https://discourse.slicer.org/t/fullscreen-the-3d-view/18403)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 2\
**Last updated:** [June 29, 2021, 5:43pm UTC](https://discourse.slicer.org/t/fullscreen-the-3d-view/18403 "2021-06-29T17:43:39Z")

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Hi, I feel this question may be naive but I searched out and didn’t find a solution for it. Here is a normal slicer window, I want to full screen the 3D view (top right window) so we can see the details better. Is …

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## [Cancel CLI module running from a loadable scripted module through clicking the cancel button of qProgressDialog](https://discourse.slicer.org/t/cancel-cli-module-running-from-a-loadable-scripted-module-through-clicking-the-cancel-button-of-qprogressdialog/18330)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 2\
**Last updated:** [June 29, 2021, 5:01pm UTC](https://discourse.slicer.org/t/cancel-cli-module-running-from-a-loadable-scripted-module-through-clicking-the-cancel-button-of-qprogressdialog/18330 "2021-06-29T17:01:05Z")

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Hi, I run a CLI module in the background in a customized loadable scripted module. And following here How to update the progress bar from a scripted CLI - #2 by strider\_hunter, I create a progressDialog to show the prog…

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## [Interactively change the nodes of mesh](https://discourse.slicer.org/t/interactively-change-the-nodes-of-mesh/18361)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 8\
**Last updated:** [June 29, 2021, 2:33pm UTC](https://discourse.slicer.org/t/interactively-change-the-nodes-of-mesh/18361 "2021-06-29T14:33:51Z")

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Hello all, Consider a mesh that is created with the segmentmesher module. For some reason, I want to change the locations of a few nodes in the created volumetric mesh to make my mesh more smooth. How can I do it? Is it…

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## [Transform Widget](https://discourse.slicer.org/t/transform-widget/18274)

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**Author:** [@Loc\_Tran](https://discourse.slicer.org/u/Loc_Tran)\
**Replies:** 2\
**Last updated:** [June 28, 2021, 8:26pm UTC](https://discourse.slicer.org/t/transform-widget/18274 "2021-06-28T20:26:08Z")

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Hello. I would like to display transformation fields and manipulate some visualization features of the fields such as spacing, scale factor. I tried writing a program to do that based on this document but it does not wo…

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## [Invert black/white](https://discourse.slicer.org/t/invert-black-white/18382)

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**Author:** [@johanna](https://discourse.slicer.org/u/johanna)\
**Replies:** 6\
**Last updated:** [June 28, 2021, 8:15pm UTC](https://discourse.slicer.org/t/invert-black-white/18382 "2021-06-28T20:15:48Z")

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Hello! Sorry if this question has been asked before - I wasn’t able to find anything. How can I invert black and white for MRI? I found this: The simplest is probably to invert your image by using SimpleFilters module:…

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## [Segmentation editor: Filling in the gaps of Threshold](https://discourse.slicer.org/t/segmentation-editor-filling-in-the-gaps-of-threshold/18370)

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**Author:** [@reddington.15](https://discourse.slicer.org/u/reddington.15)\
**Replies:** 4\
**Last updated:** [June 28, 2021, 3:33pm UTC](https://discourse.slicer.org/t/segmentation-editor-filling-in-the-gaps-of-threshold/18370 "2021-06-28T15:33:44Z")

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Hello, I am working on isolating the pelvis from the body and it is taking me some time, so I was curious if there was a faster way in filling in the gaps in each slice of the CT scan after thresholding. I am manually g…

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## [Visualizing MRI data taken over time and taking cross sections](https://discourse.slicer.org/t/visualizing-mri-data-taken-over-time-and-taking-cross-sections/18372)

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**Author:** [@dsoto](https://discourse.slicer.org/u/dsoto)\
**Replies:** 2\
**Last updated:** [June 28, 2021, 3:20pm UTC](https://discourse.slicer.org/t/visualizing-mri-data-taken-over-time-and-taking-cross-sections/18372 "2021-06-28T15:20:43Z")

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Hello all, I’m new to using Slicer and have run into a couple issues regarding displaying MRI data. So I have multiple datasets I am working with, some of which are anatomical, taking cross sections over different sagit…

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## [How to smooth label image rendering?](https://discourse.slicer.org/t/how-to-smooth-label-image-rendering/18363)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 1\
**Last updated:** [June 28, 2021, 3:18pm UTC](https://discourse.slicer.org/t/how-to-smooth-label-image-rendering/18363 "2021-06-28T15:18:15Z")

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Hello, Fellows. I’ve done it previous 3D Slice versions, but now, I seem not to find the options anymore. (Below an example) Any help, please? Thanks.

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## [Interactive Zoom Mouse Drag Direction](https://discourse.slicer.org/t/interactive-zoom-mouse-drag-direction/17832)

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**Author:** [@spycolyf](https://discourse.slicer.org/u/spycolyf)\
**Replies:** 8\
**Last updated:** [June 28, 2021, 2:55pm UTC](https://discourse.slicer.org/t/interactive-zoom-mouse-drag-direction/17832 "2021-06-28T14:55:18Z")

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Currently, when you interactively zoom with the mouse, dragging the mouse up zooms out, and dragging down zooms in. I’m using my slicer module as an extension to a main app that zooms in the opposite direction. This conf…

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## [3DView Model Animation (Fade-in, Fade-out)](https://discourse.slicer.org/t/3dview-model-animation-fade-in-fade-out/18367)

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**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 5\
**Last updated:** [June 28, 2021, 1:56pm UTC](https://discourse.slicer.org/t/3dview-model-animation-fade-in-fade-out/18367 "2021-06-28T13:56:44Z")

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I have 2 models that are aligned. I would like to visually show them using an animation that fades-in the source model, while simultaneously fading out the target-model, say within a 1-second timeframe, then do vice-vers…

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