# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=321

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

**Page:** 322

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## [Can't clone a volume property in Data module](https://discourse.slicer.org/t/cant-clone-a-volume-property-in-data-module/13535)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 4\
**Last updated:** [September 18, 2020, 4:16pm UTC](https://discourse.slicer.org/t/cant-clone-a-volume-property-in-data-module/13535 "2020-09-18T16:16:22Z")

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I want to have clone an existing VP and then modify that (for an animation). It seems right-clicking on the volume property to clone in Data module doesn’t seem to work (in all nodes tab). Is this expected? I can save a…

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## [Apply a smooth dense deformation](https://discourse.slicer.org/t/apply-a-smooth-dense-deformation/11117)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 4\
**Last updated:** [September 18, 2020, 2:43pm UTC](https://discourse.slicer.org/t/apply-a-smooth-dense-deformation/11117 "2020-09-18T14:43:58Z")

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Hi all, I need to do the data augmentation used by the 3-D Unet work (paper link): “Besides rotation, scaling and gray value augmentation, we apply a smooth dense deformation field on both data and ground truth labels. …

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## [SimpleITK tries to write Python wrapped files into a default folder that needs root privileges](https://discourse.slicer.org/t/simpleitk-tries-to-write-python-wrapped-files-into-a-default-folder-that-needs-root-privileges/13536)

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**Author:** [@myousefi2016](https://discourse.slicer.org/u/myousefi2016)\
**Replies:** 9\
**Last updated:** [September 18, 2020, 2:35pm UTC](https://discourse.slicer.org/t/simpleitk-tries-to-write-python-wrapped-files-into-a-default-folder-that-needs-root-privileges/13536 "2020-09-18T14:35:14Z")

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I’m trying to bake Slicer 4.11 from the source and use my system installed Python 3.6. This is my cmake command: cmake -DCMAKE\_INSTALL\_PREFIX=/scratch1/yousefi/Slicer-Install/ -DSlicer\_USE\_SYSTEM\_python=ON -DSlicer\_USE\_…

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## [3D view saving problem](https://discourse.slicer.org/t/3d-view-saving-problem/13541)

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**Author:** [@opetne](https://discourse.slicer.org/u/opetne)\
**Replies:** 0\
**Last updated:** [September 18, 2020, 10:20am UTC](https://discourse.slicer.org/t/3d-view-saving-problem/13541 "2020-09-18T10:20:49Z")

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4.11.0 version If I want to save a screenshot of the 3D view only a small blue strip is saved. I tried to save the 3D view with transparent background as well with this script: renderWindow = slicer.app.layoutManager()…

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## [Annotations in 3D slicer to prepare training datasets](https://discourse.slicer.org/t/annotations-in-3d-slicer-to-prepare-training-datasets/13528)

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**Author:** [@Jigabytes](https://discourse.slicer.org/u/Jigabytes)\
**Replies:** 1\
**Last updated:** [September 18, 2020, 12:21am UTC](https://discourse.slicer.org/t/annotations-in-3d-slicer-to-prepare-training-datasets/13528 "2020-09-18T00:21:08Z")

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Hi,Can we use 3D Slicer to do annotation on medical image slices and then prepare annotated data to build training data sets to build neural network from scratch? Can you point me to tutorial or example of it?

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## ['SegmentEditorEffect' object has no attribute 'segmentMarkupNode'](https://discourse.slicer.org/t/segmenteditoreffect-object-has-no-attribute-segmentmarkupnode/13440)

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**Author:** [@Anand\_Mulay](https://discourse.slicer.org/u/Anand_Mulay)\
**Replies:** 4\
**Last updated:** [September 18, 2020, 12:03am UTC](https://discourse.slicer.org/t/segmenteditoreffect-object-has-no-attribute-segmentmarkupnode/13440 "2020-09-18T00:03:54Z")

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I’m trying to use Nvidia Ai using the sample script (https://gist.github.com/lassoan/ef30bc27a22a648ead7f82243f5cc7d5) First I got an internal error for the study which is running successfully in the editor but not with…

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## [How to modify the content of "data probe" using python script](https://discourse.slicer.org/t/how-to-modify-the-content-of-data-probe-using-python-script/13524)

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**Author:** [@valery](https://discourse.slicer.org/u/valery)\
**Replies:** 1\
**Last updated:** [September 17, 2020, 7:48pm UTC](https://discourse.slicer.org/t/how-to-modify-the-content-of-data-probe-using-python-script/13524 "2020-09-17T19:48:40Z")

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Hi everybody, I’m looking for a bit of help. I would like to modify the content of “data probe” in python script inside Slicer. For instance : how to activate the colorbar on the overlay enable/disable corner text an…

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## ["Probe volume with model" error](https://discourse.slicer.org/t/probe-volume-with-model-error/13529)

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**Author:** [@janneke\_slicer](https://discourse.slicer.org/u/janneke_slicer)\
**Replies:** 2\
**Last updated:** [September 17, 2020, 5:51pm UTC](https://discourse.slicer.org/t/probe-volume-with-model-error/13529 "2020-09-17T17:51:41Z")

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Hello, I want to probe a displacement field (vector volume) with a model with the “Probe volume with model” module in Slicer 4.11.0. So I want that each point on the mesh/model contains the corresponding x-, y-, and z-v…

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## [Adding many models to hierarchy](https://discourse.slicer.org/t/adding-many-models-to-hierarchy/13513)

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**Author:** [@mfolson](https://discourse.slicer.org/u/mfolson)\
**Replies:** 2\
**Last updated:** [September 17, 2020, 4:09pm UTC](https://discourse.slicer.org/t/adding-many-models-to-hierarchy/13513 "2020-09-17T16:09:57Z")

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I am trying to create a label map for 100+ STLs. I was able to do this by importing all STLs as models, grouping them under a model hierarchy, importing the model hierarchy as a segmentation, and then exporting that segm…

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## [how to automatically segment bones from dicom](https://discourse.slicer.org/t/how-to-automatically-segment-bones-from-dicom/13507)

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**Author:** [@Matt\_Dean](https://discourse.slicer.org/u/Matt_Dean)\
**Replies:** 2\
**Last updated:** [September 17, 2020, 4:07pm UTC](https://discourse.slicer.org/t/how-to-automatically-segment-bones-from-dicom/13507 "2020-09-17T16:07:50Z")

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Hi, I have dicom files with multiple (separate) bones scanned at once. I want to automatically segment each bone and create a watertight surface mesh (ply format) for each bone. All the tutorials I am finding require man…

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## [Split Scalar Volume into Multiple Frames](https://discourse.slicer.org/t/split-scalar-volume-into-multiple-frames/13490)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 8\
**Last updated:** [September 17, 2020, 1:42pm UTC](https://discourse.slicer.org/t/split-scalar-volume-into-multiple-frames/13490 "2020-09-17T13:42:55Z")

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Hello, I am trying to split scalar-DICOM volume, with multiple frames, so that I can create multiple volumes. I am trying to do this because the multi-volume exporter does not seem to recognize the input volume as a mu…

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## [Centering slice view not going to center of transformed volume](https://discourse.slicer.org/t/centering-slice-view-not-going-to-center-of-transformed-volume/13485)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 6\
**Last updated:** [September 17, 2020, 1:13pm UTC](https://discourse.slicer.org/t/centering-slice-view-not-going-to-center-of-transformed-volume/13485 "2020-09-17T13:13:49Z")

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I loaded a 2D sequence volume and created a transform to apply to the sequence setting spacing for X, Y, and Z dimensions. Z was set to 0.2mm from a default of 1.0mm. However, centering the axial red slice after applyi…

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## [Extraction of artery radius along the centerline ](https://discourse.slicer.org/t/extraction-of-artery-radius-along-the-centerline/13527)

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**Author:** [@irnjsn](https://discourse.slicer.org/u/irnjsn)\
**Replies:** 1\
**Last updated:** [September 17, 2020, 12:41pm UTC](https://discourse.slicer.org/t/extraction-of-artery-radius-along-the-centerline/13527 "2020-09-17T12:41:44Z")

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Hi everyone, I realized a segmentation of the femoral artery and used Extract Centerline to obtain the coordinates of the centerline. The data extracted from this centerline gives a radius (I guess an average one) of th…

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## [Shortcut for Sphere brush](https://discourse.slicer.org/t/shortcut-for-sphere-brush/13460)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 2\
**Last updated:** [September 17, 2020, 12:26pm UTC](https://discourse.slicer.org/t/shortcut-for-sphere-brush/13460 "2020-09-17T12:26:04Z")

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I’m trying to set up a key shortcut in python to enable/disable sphere brush in PaintEffect. The first step is code to set that parameter, which I’m doing like this: segmentEditorWidget = slicer.qMRMLSegmentEditorWidget…

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## [Getting volume coordinates from RAS coords](https://discourse.slicer.org/t/getting-volume-coordinates-from-ras-coords/13517)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [September 17, 2020, 11:46am UTC](https://discourse.slicer.org/t/getting-volume-coordinates-from-ras-coords/13517 "2020-09-17T11:46:47Z")

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How can I get x,y,z coordinates as per the raw slice data from RAS coordinates? We are choosing a point in the interactor screen and would like to know its position according to x,y,z points of raw slice data.

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## [Is 3Dslicer working with GPU ?](https://discourse.slicer.org/t/is-3dslicer-working-with-gpu/13523)

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**Author:** [@Eyck\_Blank](https://discourse.slicer.org/u/Eyck_Blank)\
**Replies:** 2\
**Last updated:** [September 17, 2020, 11:41am UTC](https://discourse.slicer.org/t/is-3dslicer-working-with-gpu/13523 "2020-09-17T11:41:59Z")

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Is 3Dslicer working with GPU ? Which GPU’s are supported ? Thank you!

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## [How to hide module GUI Panel?](https://discourse.slicer.org/t/how-to-hide-module-gui-panel/13520)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [September 17, 2020, 11:35am UTC](https://discourse.slicer.org/t/how-to-hide-module-gui-panel/13520 "2020-09-17T11:35:37Z")

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How can I hide the module GUI panel? I was able to hide all the bars but can’t hide the GUI with this welcome label on the left.

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## [Loading stopped at AutoStru](https://discourse.slicer.org/t/loading-stopped-at-autostru/13493)

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**Author:** [@Eyck\_Blank](https://discourse.slicer.org/u/Eyck_Blank)\
**Replies:** 6\
**Last updated:** [September 17, 2020, 9:46am UTC](https://discourse.slicer.org/t/loading-stopped-at-autostru/13493 "2020-09-17T09:46:23Z")

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Hi, I cannot load pation DICOM files into 3D Slicer, independent od AdvanceMode is checked. . I use version 4.10.2 The loading process will stopped at AutoStru. Could someone help me?

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## [Visualize .igs.mha tracked ultrasound sequence in 3D](https://discourse.slicer.org/t/visualize-igs-mha-tracked-ultrasound-sequence-in-3d/11835)

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**Author:** [@Tonight1121](https://discourse.slicer.org/u/Tonight1121)\
**Replies:** 8\
**Last updated:** [September 17, 2020, 2:47am UTC](https://discourse.slicer.org/t/visualize-igs-mha-tracked-ultrasound-sequence-in-3d/11835 "2020-09-17T02:47:36Z")

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Hi! I am new to the Slicer and I am trying to visualize some seqeunce file examples shared in PlusDataLib repository. While I load the SpineUltrasound-Lumbar-C5.igs.mha as Sequence Metafile into the Sequence browser, it…

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## [Slicer/Jupyter integration: installing python packages](https://discourse.slicer.org/t/slicer-jupyter-integration-installing-python-packages/13386)

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**Author:** [@yoomi](https://discourse.slicer.org/u/yoomi)\
**Replies:** 29\
**Last updated:** [September 17, 2020, 2:07am UTC](https://discourse.slicer.org/t/slicer-jupyter-integration-installing-python-packages/13386 "2020-09-17T02:07:17Z")

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Hello, I’m having trouble integrating 3D Slicer with Jupyter on my computer. I installed both Slicer and Jupyter, but am stuck on installing python packages. When I paste the below into the python interactor in Slicer a…

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## [Segmentation size](https://discourse.slicer.org/t/segmentation-size/13509)

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**Author:** [@MAM](https://discourse.slicer.org/u/MAM)\
**Replies:** 1\
**Last updated:** [September 17, 2020, 12:21am UTC](https://discourse.slicer.org/t/segmentation-size/13509 "2020-09-17T00:21:03Z")

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Operating system: Windows 10 Slicer version: 4.10.2 I’d like to save my segmentation with the same size in nifti format. When I go through Segmentation\\ export\\advanced and choose a reference volume, I can’t save in ni…

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## [Segmentation Storage: 1.2.840.10008.5.1.4.1.1.66.4](https://discourse.slicer.org/t/segmentation-storage-1-2-840-10008-5-1-4-1-1-66-4/4274)

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**Author:** [@malaterre](https://discourse.slicer.org/u/malaterre)\
**Replies:** 21\
**Last updated:** [September 16, 2020, 3:34pm UTC](https://discourse.slicer.org/t/segmentation-storage-1-2-840-10008-5-1-4-1-1-66-4/4274 "2020-09-16T15:34:12Z")

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Hi there, I am browsing through the paper: DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer researc…

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## [Smooth the surface of a segment created from stl file](https://discourse.slicer.org/t/smooth-the-surface-of-a-segment-created-from-stl-file/12341)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 12\
**Last updated:** [September 16, 2020, 1:45am UTC](https://discourse.slicer.org/t/smooth-the-surface-of-a-segment-created-from-stl-file/12341 "2020-09-16T01:45:11Z")

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Hello, I tried to use median smoothing in Segment Editor on a segment node created from an stl input. However, after ~15 min smoothing task didn’t complete. Could someone look into it? I am trying to smooth this seg…

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## [Segmentation does not display in a 3D view](https://discourse.slicer.org/t/segmentation-does-not-display-in-a-3d-view/13473)

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**Author:** [@whirl](https://discourse.slicer.org/u/whirl)\
**Replies:** 4\
**Last updated:** [September 15, 2020, 8:35pm UTC](https://discourse.slicer.org/t/segmentation-does-not-display-in-a-3d-view/13473 "2020-09-15T20:35:06Z")

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Hello I tried to segment bones in the following scan usung “Threshold”. Unfortunately, it does not display properly in a 3D view. There is only a small 2D visible. What I’ve done wrong? Screenshot:

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## [How to convert DTI tensor nhdr file from NRRD0004 to NRRD0005](https://discourse.slicer.org/t/how-to-convert-dti-tensor-nhdr-file-from-nrrd0004-to-nrrd0005/13016)

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**Author:** [@Xiaogai\_Li](https://discourse.slicer.org/u/Xiaogai_Li)\
**Replies:** 6\
**Last updated:** [September 15, 2020, 7:32pm UTC](https://discourse.slicer.org/t/how-to-convert-dti-tensor-nhdr-file-from-nrrd0004-to-nrrd0005/13016 "2020-09-15T19:32:05Z")

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Dear all, I wonder if there is any way to convert DTI tensor file in .nhdr format from NRRD0004 to NRRD0005? As in the header file .nhdr for tensor, NRRD0004 has a line with six components, e.g. sizes: 6 181 216 179, …

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## [Slicer display issues - green stripes](https://discourse.slicer.org/t/slicer-display-issues-green-stripes/13483)

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**Author:** [@dayanjan](https://discourse.slicer.org/u/dayanjan)\
**Replies:** 2\
**Last updated:** [September 14, 2020, 5:38pm UTC](https://discourse.slicer.org/t/slicer-display-issues-green-stripes/13483 "2020-09-14T17:38:55Z")

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Operating system: Windows 10 Pro 64 bit (10.0 build 18363) Slicer version: 4.10 Expected behavior: Normal slicer window on load Actual behavior: The display has a whole bunch of green lines going through it horizontal…

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## [Correction of MRI image distortion](https://discourse.slicer.org/t/correction-of-mri-image-distortion/13475)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 3:52pm UTC](https://discourse.slicer.org/t/correction-of-mri-image-distortion/13475 "2020-09-14T15:52:25Z")

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Slicer version:4.10.1 Hi 3D Slicer experts and all I have 2 images( CT and MRI). We calculated the displacement (distortion) of each point in MRI relative to CT image(Slicer B splin Tranform). Now, I have a question. H…

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## [Configurating Robot arm (Panda - Franka Emika) In slicer](https://discourse.slicer.org/t/configurating-robot-arm-panda-franka-emika-in-slicer/12397)

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**Author:** [@Cesar\_Puga](https://discourse.slicer.org/u/Cesar_Puga)\
**Replies:** 13\
**Last updated:** [September 14, 2020, 12:47pm UTC](https://discourse.slicer.org/t/configurating-robot-arm-panda-franka-emika-in-slicer/12397 "2020-09-14T12:47:04Z")

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I went through the ROSMED tutorials where a robot arm is loaded to perform a needle insertion, my goal is to recreate this action but with another robot arm model, from what i can see in the tutorial, i would need to get…

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## [Longitudinal registration brain MRI](https://discourse.slicer.org/t/longitudinal-registration-brain-mri/13481)

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**Author:** [@Marianne](https://discourse.slicer.org/u/Marianne)\
**Replies:** 0\
**Last updated:** [September 14, 2020, 12:28pm UTC](https://discourse.slicer.org/t/longitudinal-registration-brain-mri/13481 "2020-09-14T12:28:17Z")

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What is the best way to compare segments from MRIs with different geometry (individual scans of the same subject)? Do I have to register all the MRIs in order to compare the segments to each other? What is the easiest wa…

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## [Create a data probe for slicelet](https://discourse.slicer.org/t/create-a-data-probe-for-slicelet/13478)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 11:36am UTC](https://discourse.slicer.org/t/create-a-data-probe-for-slicelet/13478 "2020-09-14T11:36:10Z")

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How to create a data probe for a slicelet that has no main window? I had tried code given in nightly scripted modules,but it is only working in presence of main window only,

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