# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=221

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

**Page:** 222

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## [SlicerIGT module loading issue](https://discourse.slicer.org/t/slicerigt-module-loading-issue/23643)

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**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 9\
**Last updated:** [June 3, 2022, 11:07am UTC](https://discourse.slicer.org/t/slicerigt-module-loading-issue/23643 "2022-06-03T11:07:49Z")

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I’m trying to use the latest SlicerIGT, which now requires SlicerIGSIO. I use the latest of this as well. I have Slicer built in release mode, from May 5 (this hash). I built SlicerIGSIO and SlicerIGT with the default …

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## [Gray color segment is appearing after performing following operation](https://discourse.slicer.org/t/gray-color-segment-is-appearing-after-performing-following-operation/23682)

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**Author:** [@Dwij\_Mistry](https://discourse.slicer.org/u/Dwij_Mistry)\
**Replies:** 1\
**Last updated:** [June 2, 2022, 12:59pm UTC](https://discourse.slicer.org/t/gray-color-segment-is-appearing-after-performing-following-operation/23682 "2022-06-02T12:59:40Z")

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Add segment → open threshold effect → delete segment → now add segment (This segment is gray color.) Note: there is no gray color in the color table

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## [Coordinates registered on DICOM](https://discourse.slicer.org/t/coordinates-registered-on-dicom/23578)

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**Author:** [@Takahashi](https://discourse.slicer.org/u/Takahashi)\
**Replies:** 16\
**Last updated:** [June 2, 2022, 11:47am UTC](https://discourse.slicer.org/t/coordinates-registered-on-dicom/23578 "2022-06-02T11:47:11Z")

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I want to integrate the coordinates acquired by 3DSlicer and Checkpoint software (Stratovan) in one file. Before integrating, I checked the coherence of coordinates for several anatomical landmarks registered with the t…

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## [What are 'logics' in Slicer](https://discourse.slicer.org/t/what-are-logics-in-slicer/23679)

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**Author:** [@gzt036](https://discourse.slicer.org/u/gzt036)\
**Replies:** 1\
**Last updated:** [June 1, 2022, 10:05pm UTC](https://discourse.slicer.org/t/what-are-logics-in-slicer/23679 "2022-06-01T22:05:24Z")

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I am new to Slicer and I am confused with the class names, could someone help to explain what is ‘loadable’, what is ‘logics’ in plain language? I mean, what is the idea using ‘Logics’ as class name? Thanks!

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## [How can I save whole heart without empty spaces?](https://discourse.slicer.org/t/how-can-i-save-whole-heart-without-empty-spaces/23596)

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**Author:** [@Js165](https://discourse.slicer.org/u/Js165)\
**Replies:** 19\
**Last updated:** [June 1, 2022, 8:30pm UTC](https://discourse.slicer.org/t/how-can-i-save-whole-heart-without-empty-spaces/23596 "2022-06-01T20:30:26Z")

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I am facing this problem while saving/exporting the segmentation into a binary label map. The problem is with HEART only. The heart contains multiple substructures. When I am saving the whole Heart and multiple substruct…

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## [Grow-cut algorithm explanation](https://discourse.slicer.org/t/grow-cut-algorithm-explanation/23670)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 6\
**Last updated:** [June 1, 2022, 6:49pm UTC](https://discourse.slicer.org/t/grow-cut-algorithm-explanation/23670 "2022-06-01T18:49:54Z")

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Hi all, I have been working lately with the grow-cut algorithm of local threshold. I find it very useful but I can’t figure out how the algorithm works on a code basis, is there any documentation on this? Thanks, Belé…

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## [Load sequence of PNG images associated with textfile with transforms](https://discourse.slicer.org/t/load-sequence-of-png-images-associated-with-textfile-with-transforms/23673)

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**Author:** [@Ale\_Ballester](https://discourse.slicer.org/u/Ale_Ballester)\
**Replies:** 0\
**Last updated:** [June 1, 2022, 2:52pm UTC](https://discourse.slicer.org/t/load-sequence-of-png-images-associated-with-textfile-with-transforms/23673 "2022-06-01T14:52:54Z")

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Hello! I am new to 3D Slicer. I have PNG images names 0.png, 1.png, etc. representing ultrasound frames taken at 100fps. For each image, there is a corresponding line in a textfile in the form (framenumber,timestamp,tra…

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## [About screen coordinates](https://discourse.slicer.org/t/about-screen-coordinates/23662)

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**Author:** [@Changing](https://discourse.slicer.org/u/Changing)\
**Replies:** 1\
**Last updated:** [June 1, 2022, 2:12pm UTC](https://discourse.slicer.org/t/about-screen-coordinates/23662 "2022-06-01T14:12:09Z")

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Hello. Through the screenshot function of 3D slicer, I extracted an image from the green view. The shape of the extracted image is 634\*441. The extracted image is displayed by opencv. The shape of the volume input to …

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## [Opening ExtensionManager while running Slicer as root crashes the app](https://discourse.slicer.org/t/opening-extensionmanager-while-running-slicer-as-root-crashes-the-app/23666)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 2\
**Last updated:** [June 1, 2022, 2:00pm UTC](https://discourse.slicer.org/t/opening-extensionmanager-while-running-slicer-as-root-crashes-the-app/23666 "2022-06-01T14:00:18Z")

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I have a setup where Slicer is run as root from within a docker container. When I try to open Extension Manager, I get a crash with the latest stable Slicer. Is this expected?

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## [Extension Manager not displaying correctly in MacOS Light Mode](https://discourse.slicer.org/t/extension-manager-not-displaying-correctly-in-macos-light-mode/23478)

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**Author:** [@Doodads](https://discourse.slicer.org/u/Doodads)\
**Replies:** 4\
**Last updated:** [June 1, 2022, 11:38am UTC](https://discourse.slicer.org/t/extension-manager-not-displaying-correctly-in-macos-light-mode/23478 "2022-06-01T11:38:27Z")

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MacOS Version: 12.2.1 Slicer Version: 4.11.20210226 Opening the extension manager with “Dark” display mode switched off on MacOS 12.2.1 shows a mostly white window; this is fixed when “Dark” mode is switched on. (see i…

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## [How to fill gaps locally? ](https://discourse.slicer.org/t/how-to-fill-gaps-locally/23657)

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**Author:** [@dbgraf20](https://discourse.slicer.org/u/dbgraf20)\
**Replies:** 1\
**Last updated:** [May 31, 2022, 10:24pm UTC](https://discourse.slicer.org/t/how-to-fill-gaps-locally/23657 "2022-05-31T22:24:23Z")

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Operating system: Windows 11 Slicer version: 4.11 Expected behavior: Clean Aorta Segmentation Actual behavior: I am segmenting several Aortas. This one is behaving rather differently. When I manually make the ROI f…

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## [Load PET.reg.lta freesurfer corregistration file in 3D slicer 4.11](https://discourse.slicer.org/t/load-pet-reg-lta-freesurfer-corregistration-file-in-3d-slicer-4-11/23616)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 2\
**Last updated:** [May 31, 2022, 6:24pm UTC](https://discourse.slicer.org/t/load-pet-reg-lta-freesurfer-corregistration-file-in-3d-slicer-4-11/23616 "2022-05-31T18:24:05Z")

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Hi: I corregistered a PET file to a freesurfer data using mri\_coreg command. I imported the freesurfer-generated data to 3D Slicer. How can I import the PET.reg.lta file in 3D Slicer? Sincerely, Gonzalo Rojas Costa

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## [The saved segmentation file size is different from the original volume nrrd file size](https://discourse.slicer.org/t/the-saved-segmentation-file-size-is-different-from-the-original-volume-nrrd-file-size/23644)

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**Author:** [@parijat\_patel](https://discourse.slicer.org/u/parijat_patel)\
**Replies:** 4\
**Last updated:** [May 31, 2022, 10:17am UTC](https://discourse.slicer.org/t/the-saved-segmentation-file-size-is-different-from-the-original-volume-nrrd-file-size/23644 "2022-05-31T10:17:12Z")

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Hello, I am using Slicer-4.11.20210226-linux-amd64 to create segmentations data to train a segmentation algorithm to automatically segment the fat depots in CT scan. The dimensions of the saved 3D segmentation file (rows…

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## [Is it possible to make the surface of the created model look like real bone?](https://discourse.slicer.org/t/is-it-possible-to-make-the-surface-of-the-created-model-look-like-real-bone/23621)

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**Author:** [@wonseok0128](https://discourse.slicer.org/u/wonseok0128)\
**Replies:** 3\
**Last updated:** [May 31, 2022, 9:52am UTC](https://discourse.slicer.org/t/is-it-possible-to-make-the-surface-of-the-created-model-look-like-real-bone/23621 "2022-05-31T09:52:29Z")

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Is it possible to make the surface of the created model look like real bone? I made humerus & hill sahcs lesion by using segment editor, growth from seeds and smoothing effect. But it looks like toy of bone… I want to…

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## [SEEG electrodes](https://discourse.slicer.org/t/seeg-electrodes/23630)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 3\
**Last updated:** [May 31, 2022, 4:54am UTC](https://discourse.slicer.org/t/seeg-electrodes/23630 "2022-05-31T04:54:48Z")

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I have the MPRAGE volume and its segmentation done with Freesurfer. What is a good way to plan the SEEG electrode position using 3DSlicer? Any module or extension?

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## [Multiprocessing is not working when PyQt widgets , DataProbe and DicomLib are used.](https://discourse.slicer.org/t/multiprocessing-is-not-working-when-pyqt-widgets-dataprobe-and-dicomlib-are-used/23595)

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**Author:** [@roopesh](https://discourse.slicer.org/u/roopesh)\
**Replies:** 2\
**Last updated:** [May 31, 2022, 4:08am UTC](https://discourse.slicer.org/t/multiprocessing-is-not-working-when-pyqt-widgets-dataprobe-and-dicomlib-are-used/23595 "2022-05-31T04:08:54Z")

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I am running an algorithm in a python script using command line with --python-script command, which has a custom button created in slicer UI, when I trigger this button , algorithm will start, which is using multiproces…

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## [Non-linear transforms not supported for volume rendering?](https://discourse.slicer.org/t/non-linear-transforms-not-supported-for-volume-rendering/23647)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [May 31, 2022, 12:38am UTC](https://discourse.slicer.org/t/non-linear-transforms-not-supported-for-volume-rendering/23647 "2022-05-31T00:38:44Z")

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I am using the Fiducial Registration Wizard to make a visual. When I choose the resultant transform as warping and set to store in a transform (not linear transform), I am getting this error when I try to apply this tra…

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## [Crop fMRI scans with a 3D mask](https://discourse.slicer.org/t/crop-fmri-scans-with-a-3d-mask/23444)

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**Author:** [@AdrienW](https://discourse.slicer.org/u/AdrienW)\
**Replies:** 3\
**Last updated:** [May 30, 2022, 8:47pm UTC](https://discourse.slicer.org/t/crop-fmri-scans-with-a-3d-mask/23444 "2022-05-30T20:47:59Z")

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Hello, I’m working on python 3.9. I would like the crop the skull of fMRI scans based on a mask created based on anatomical data. The dimensions of the mask is 181 x 217 X 181. My fMRI scans are 4D time-series data wit…

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## [How to export distances between anatomical landmarks](https://discourse.slicer.org/t/how-to-export-distances-between-anatomical-landmarks/23489)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [May 30, 2022, 8:44pm UTC](https://discourse.slicer.org/t/how-to-export-distances-between-anatomical-landmarks/23489 "2022-05-30T20:44:35Z")

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Operating system:win10 Slicer version: r29738 Dear slicerMorph user, I am wondering if there is a way to export the dimensions between anatomical landmarks. General worklfow in slicerMorph List item data acquisiti…

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## [DynamicModeler Transform Maker](https://discourse.slicer.org/t/dynamicmodeler-transform-maker/23626)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 9\
**Last updated:** [May 30, 2022, 4:03pm UTC](https://discourse.slicer.org/t/dynamicmodeler-transform-maker/23626 "2022-05-30T16:03:27Z")

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I already started implementing. The idea is a transformComposer that would get as input any number of: oneFiducialLists, angles, planes and linearTransforms. It would concatenate the transform for all of them. And outp…

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## [Rotational transformation matrix after surface registration](https://discourse.slicer.org/t/rotational-transformation-matrix-after-surface-registration/21813)

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**Author:** [@mdhan](https://discourse.slicer.org/u/mdhan)\
**Replies:** 3\
**Last updated:** [May 30, 2022, 2:13pm UTC](https://discourse.slicer.org/t/rotational-transformation-matrix-after-surface-registration/21813 "2022-05-30T14:13:40Z")

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Hello, I’m rather new to 3D Slicer, and I’d greatly appreciate any advice! I am interested in obtaining the rotational transformation matrix after registering one model to another. For registration, I used the Slicer CM…

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## [How to implement this interface](https://discourse.slicer.org/t/how-to-implement-this-interface/23579)

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**Author:** [@wanghao1](https://discourse.slicer.org/u/wanghao1)\
**Replies:** 2\
**Last updated:** [May 30, 2022, 7:03am UTC](https://discourse.slicer.org/t/how-to-implement-this-interface/23579 "2022-05-30T07:03:57Z")

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I saw this example on the Plus website.This is a simple test application to visualize all the tracker tools and the numerical values of the acquired transforms. The visualized data can be optionally saved into file.Is…

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## [\_Failed to connect to server 127.0.0.1:4100](https://discourse.slicer.org/t/failed-to-connect-to-server-127-0-0-1-4100/15095)

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**Author:** [@DimaLat](https://discourse.slicer.org/u/DimaLat)\
**Replies:** 1\
**Last updated:** [May 30, 2022, 1:15am UTC](https://discourse.slicer.org/t/failed-to-connect-to-server-127-0-0-1-4100/15095 "2022-05-30T01:15:35Z")

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Operating system: Windows 10 Slicer version: 4.11 Expected behavior: Matlab bridge executes Matlab properly Actual behavior: There is an error calling Matlab Debug: In D:\\D\\P\\S-0-E-b\\SlicerOpenIGTLink-build\\OpenIGTLi…

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## [DICOM sort method](https://discourse.slicer.org/t/dicom-sort-method/23592)

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**Author:** [@Hu-nie](https://discourse.slicer.org/u/Hu-nie)\
**Replies:** 3\
**Last updated:** [May 27, 2022, 4:37am UTC](https://discourse.slicer.org/t/dicom-sort-method/23592 "2022-05-27T04:37:22Z")

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I have a question about DICOM. I am dealing with MR images. At this time, I try to use the Instance Number when aligning the DICOM. When I look at the Type of Instance Number Tag, it says “Required, Empty if Unknown (2…

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## [apply a deformable registration from a REG-DICOM file](https://discourse.slicer.org/t/apply-a-deformable-registration-from-a-reg-dicom-file/23329)

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**Author:** [@ssm](https://discourse.slicer.org/u/ssm)\
**Replies:** 5\
**Last updated:** [May 29, 2022, 3:40am UTC](https://discourse.slicer.org/t/apply-a-deformable-registration-from-a-reg-dicom-file/23329 "2022-05-29T03:40:35Z")

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Hi, the Transforms module is only capable of creating new volumes from a REG-DICOM import for registration done in Velocity or Eclipse but not for deformable registrations. Could you help me?

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## [Dynamic modeler: Add model, Glyph and Boolean Operations](https://discourse.slicer.org/t/dynamic-modeler-add-model-glyph-and-boolean-operations/23420)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 6\
**Last updated:** [May 29, 2022, 1:13am UTC](https://discourse.slicer.org/t/dynamic-modeler-add-model-glyph-and-boolean-operations/23420 "2022-05-29T01:13:58Z")

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Hi devs and users. I would be interesting in developing Dinamyc Modeler’s tools for: adding parametric models for all available vtkSourceFilters that give a 3d mesh. also adding a glyph tool that according to markup po…

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## [Remove CT patient bed from dicom file automatically](https://discourse.slicer.org/t/remove-ct-patient-bed-from-dicom-file-automatically/23614)

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**Author:** [@gzt036](https://discourse.slicer.org/u/gzt036)\
**Replies:** 5\
**Last updated:** [May 28, 2022, 11:58am UTC](https://discourse.slicer.org/t/remove-ct-patient-bed-from-dicom-file-automatically/23614 "2022-05-28T11:58:37Z")

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Is it possible to remove CT bed background noise from DICOM automatically without opening Slicer’s graphic window? The python script needs to be run by the server so human intervene needs to be avoided. My question is, …

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## [What is fcsv file?](https://discourse.slicer.org/t/what-is-fcsv-file/23608)

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**Author:** [@Ti\_n\_D\_t\_Ha](https://discourse.slicer.org/u/Ti_n_D_t_Ha)\
**Replies:** 3\
**Last updated:** [May 28, 2022, 11:50am UTC](https://discourse.slicer.org/t/what-is-fcsv-file/23608 "2022-05-28T11:50:36Z")

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I’m using the ALPACA module in SlicerMorph extensions to align the 3D model to CTCB anatomy. In the video there is a .fcsv file for the ‘Source Lanmarks’, but I don’t know how to export the STL file to the .fcsv file. O…

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## [Transfrom parralel to a line](https://discourse.slicer.org/t/transfrom-parralel-to-a-line/23607)

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**Author:** [@Igor\_S](https://discourse.slicer.org/u/Igor_S)\
**Replies:** 3\
**Last updated:** [May 28, 2022, 10:45am UTC](https://discourse.slicer.org/t/transfrom-parralel-to-a-line/23607 "2022-05-28T10:45:59Z")

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Operating system: Windows Slicer version: 5.1. Hello, I have to orient a CT image according to two lines. So right now i manually transform-rotate image so that the image is oriented parallel to the first line in axia…

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## [Slice Thickness for multi-frame ultrasound](https://discourse.slicer.org/t/slice-thickness-for-multi-frame-ultrasound/23617)

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**Author:** [@svesal](https://discourse.slicer.org/u/svesal)\
**Replies:** 3\
**Last updated:** [May 28, 2022, 12:30am UTC](https://discourse.slicer.org/t/slice-thickness-for-multi-frame-ultrasound/23617 "2022-05-28T00:30:00Z")

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Hi, I am just new to 3D slicer and I wanted to ask one question. I have a set of raw ultrasound data (cineloop) and I have the pixel spacing information (0.03x0.03) and not slice thickness for volumetric reconstruction.…

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