# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=240

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

**Page:** 241

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## [Open two python interactors](https://discourse.slicer.org/t/open-two-python-interactors/21780)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 0\
**Last updated:** [February 3, 2022, 4:03pm UTC](https://discourse.slicer.org/t/open-two-python-interactors/21780 "2022-02-03T16:03:12Z")

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Hi all, I have a script with four steps in order to segment different coronary regions. I need my script to wait so I can manually do the segmentation. Is there any way I can run the script, let it waiting and then wake…

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## [Change value of label for segmentation](https://discourse.slicer.org/t/change-value-of-label-for-segmentation/21772)

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**Author:** [@codeenthusiast](https://discourse.slicer.org/u/codeenthusiast)\
**Replies:** 2\
**Last updated:** [February 3, 2022, 12:56pm UTC](https://discourse.slicer.org/t/change-value-of-label-for-segmentation/21772 "2022-02-03T12:56:54Z")

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Operating system: MacOS Slicer version: 4.11 Hi there, I am developing a script to perform radiomics extraction from a set of images with associated segmentations. Unfortunately, the label values are inconsistent in t…

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## [Watershed, Fast marching, and Flood filling effects in Segment editor](https://discourse.slicer.org/t/watershed-fast-marching-and-flood-filling-effects-in-segment-editor/104)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 17\
**Last updated:** [February 22, 2019, 2:37pm UTC](https://discourse.slicer.org/t/watershed-fast-marching-and-flood-filling-effects-in-segment-editor/104 "2019-02-22T14:37:34Z")

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Three semi-automatic segmentation effects have added to the Segment editor. They are available in the latest nightly build, by installing the new SegmentEditorExtraEffects extension: They are all semi-automatic method…

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## [segmentation different structure of individual tooth](https://discourse.slicer.org/t/segmentation-different-structure-of-individual-tooth/13374)

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**Author:** [@HAFIZAL](https://discourse.slicer.org/u/HAFIZAL)\
**Replies:** 18\
**Last updated:** [February 3, 2022, 4:32am UTC](https://discourse.slicer.org/t/segmentation-different-structure-of-individual-tooth/13374 "2022-02-03T04:32:29Z")

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Hi guys, I am new with this app. I did try the watershed effect for tooth segmentation. I am going to do a research project measuring volume of the tooth. But, my area of interest is the different structure of teeth, spe…

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## [Remove islands inside the resulting STL from a segment](https://discourse.slicer.org/t/remove-islands-inside-the-resulting-stl-from-a-segment/21752)

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**Author:** [@anon29823344](https://discourse.slicer.org/u/anon29823344)\
**Replies:** 2\
**Last updated:** [February 3, 2022, 1:13am UTC](https://discourse.slicer.org/t/remove-islands-inside-the-resulting-stl-from-a-segment/21752 "2022-02-03T01:13:17Z")

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Operating system: Windows 10 Pro. Version: 21H2. Build: 19044.1466 Slicer version: 4.11.20210226 r29738 / 7a593c8 Hello all. This is my first question in the forum, so I hope this topic is not repeated (at least I cou…

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## [How to import fiducials from table](https://discourse.slicer.org/t/how-to-import-fiducials-from-table/21761)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [February 2, 2022, 6:35pm UTC](https://discourse.slicer.org/t/how-to-import-fiducials-from-table/21761 "2022-02-02T18:35:37Z")

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I have csv file that is in LPS coordinates. I loaded the table to Slicer, when I use the import functionality of the Markups tool to save them in a PointList object, the coordinates all show as 0,0,0. There is an error m…

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## [Measuring distance between markers in 2 different scans, struggling with transform because of unknown segment origins?](https://discourse.slicer.org/t/measuring-distance-between-markers-in-2-different-scans-struggling-with-transform-because-of-unknown-segment-origins/21717)

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**Author:** [@tbmeier](https://discourse.slicer.org/u/tbmeier)\
**Replies:** 4\
**Last updated:** [February 2, 2022, 5:51pm UTC](https://discourse.slicer.org/t/measuring-distance-between-markers-in-2-different-scans-struggling-with-transform-because-of-unknown-segment-origins/21717 "2022-02-02T17:51:51Z")

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I have MRI scans of the knee (femur and tibia) and I am looking to compare the position of fiducials on the skin with respect to the bone between 2 different scans. I have segmented each bone in both scans, and then I s…

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## [Open a slicer module with python](https://discourse.slicer.org/t/open-a-slicer-module-with-python/21754)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 3\
**Last updated:** [February 2, 2022, 4:48pm UTC](https://discourse.slicer.org/t/open-a-slicer-module-with-python/21754 "2022-02-02T16:48:49Z")

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I want to open my custom scripted module every time I open Slicer. I know that I have to edit the .slicerrc.py file, but I don’t know what lines of code to put in there.

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## [Segment terminology dialog box: remember user's choice about displaying advanced terminology](https://discourse.slicer.org/t/segment-terminology-dialog-box-remember-users-choice-about-displaying-advanced-terminology/21738)

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**Author:** [@chribaue](https://discourse.slicer.org/u/chribaue)\
**Replies:** 3\
**Last updated:** [February 2, 2022, 1:33pm UTC](https://discourse.slicer.org/t/segment-terminology-dialog-box-remember-users-choice-about-displaying-advanced-terminology/21738 "2022-02-02T13:33:35Z")

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I have a request regarding the dialog box used to edit “color and terminology codes” of segments. In modules “Segmentations” and “Segment Editor” a double click on the color opens the following dialog: with the left …

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## [Is there an API for RPC?](https://discourse.slicer.org/t/is-there-an-api-for-rpc/21734)

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**Author:** [@swirlsky](https://discourse.slicer.org/u/swirlsky)\
**Replies:** 4\
**Last updated:** [February 2, 2022, 1:29pm UTC](https://discourse.slicer.org/t/is-there-an-api-for-rpc/21734 "2022-02-02T13:29:59Z")

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I’m wondering if there’s a way to instruct slicer from a remote application to load e.g. a DICOM Study or do other operations. Like OsiriX has one: http://www.osirix-viewer.com/HIS-Integration.pdf

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## [Problem in loading volume rendering automatically](https://discourse.slicer.org/t/problem-in-loading-volume-rendering-automatically/21747)

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**Author:** [@user5](https://discourse.slicer.org/u/user5)\
**Replies:** 4\
**Last updated:** [February 2, 2022, 12:58pm UTC](https://discourse.slicer.org/t/problem-in-loading-volume-rendering-automatically/21747 "2022-02-02T12:58:03Z")

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I would like to load the volume rendering automatically when I open the Slicer. I follow the code in this link, but the volume rendering cannot load automatically. https://slicer.readthedocs.io/en/latest/developer\_guid…

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## [Crosshair vs Slice Intersections](https://discourse.slicer.org/t/crosshair-vs-slice-intersections/21700)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 10\
**Last updated:** [February 2, 2022, 5:42am UTC](https://discourse.slicer.org/t/crosshair-vs-slice-intersections/21700 "2022-02-02T05:42:29Z")

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What is the difference between the “Crosshair” versus using “Slice Intersections”? They seem to be the same type thing, but they are two different objects so it is a bit confusing about which one to use. There is the Cr…

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## [Loading DICOM CT+RT Structure is incomplete](https://discourse.slicer.org/t/loading-dicom-ct-rt-structure-is-incomplete/21696)

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**Author:** [@Fabian\_Jichi](https://discourse.slicer.org/u/Fabian_Jichi)\
**Replies:** 11\
**Last updated:** [February 1, 2022, 5:43pm UTC](https://discourse.slicer.org/t/loading-dicom-ct-rt-structure-is-incomplete/21696 "2022-02-01T17:43:59Z")

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Hello, I loaded different DICOM series that already have contours that need some editing. First problem is that the loaded contour is broken sometimes like in this pictures: First I thought is just something visual…

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## [How to automatically register batch of lung CT volumes using Python and SlicerElastix extension?](https://discourse.slicer.org/t/how-to-automatically-register-batch-of-lung-ct-volumes-using-python-and-slicerelastix-extension/21727)

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**Author:** [@alan6690](https://discourse.slicer.org/u/alan6690)\
**Replies:** 0\
**Last updated:** [February 1, 2022, 11:15am UTC](https://discourse.slicer.org/t/how-to-automatically-register-batch-of-lung-ct-volumes-using-python-and-slicerelastix-extension/21727 "2022-02-01T11:15:24Z")

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I have around 100 pairs of CT lung volumes to be deformably registered by SlicerElastix extension using its “3D CT, monomodal” modality. All volumes are in nii file format. I now do it one-by-one manually. However each r…

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## [Deformation automatically inverted after centering volume](https://discourse.slicer.org/t/deformation-automatically-inverted-after-centering-volume/21597)

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**Author:** [@alan6690](https://discourse.slicer.org/u/alan6690)\
**Replies:** 7\
**Last updated:** [February 1, 2022, 11:08am UTC](https://discourse.slicer.org/t/deformation-automatically-inverted-after-centering-volume/21597 "2022-02-01T11:08:20Z")

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I have deformably register two CT volumes using the SlicerElastix extension and save the deformation transformation. The output volume is well matched with the fixed volume after the deformation as the deformation also c…

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## [Plane markup type persistance](https://discourse.slicer.org/t/plane-markup-type-persistance/21722)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 1\
**Last updated:** [February 1, 2022, 2:34am UTC](https://discourse.slicer.org/t/plane-markup-type-persistance/21722 "2022-02-01T02:34:43Z")

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Is it possible to make the plane markup type persistent, or to change the default type? I usually use the 3-point placement method, but am needing to change this for each plane, even when in persistent placement mode.

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## [Multi-trial landmarking using SlicerMorph](https://discourse.slicer.org/t/multi-trial-landmarking-using-slicermorph/21668)

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**Author:** [@anromero](https://discourse.slicer.org/u/anromero)\
**Replies:** 7\
**Last updated:** [January 31, 2022, 9:18pm UTC](https://discourse.slicer.org/t/multi-trial-landmarking-using-slicermorph/21668 "2022-01-31T21:18:30Z")

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Hello there, I’m doing a study on cranial fluctuating asymmetry and the Procrustes ANOVA that is common for statistical analysis of FA requires at minimum two landmarking trials (I typically use the geomorph package in R…

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## [vascular characteristics ](https://discourse.slicer.org/t/vascular-characteristics/21716)

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**Author:** [@Effand](https://discourse.slicer.org/u/Effand)\
**Replies:** 0\
**Last updated:** [January 31, 2022, 7:01pm UTC](https://discourse.slicer.org/t/vascular-characteristics/21716 "2022-01-31T19:01:12Z")

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Hi All, First thank you so much for such an informative forum which was a great help. After performing vessel segmentation on a new robust ultrasound images, and thanks to the help in this forum for making such a progre…

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## [Loading of 4D nrrd data - Volume Sequence not available](https://discourse.slicer.org/t/loading-of-4d-nrrd-data-volume-sequence-not-available/21633)

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**Author:** [@kafux](https://discourse.slicer.org/u/kafux)\
**Replies:** 7\
**Last updated:** [January 31, 2022, 10:38am UTC](https://discourse.slicer.org/t/loading-of-4d-nrrd-data-volume-sequence-not-available/21633 "2022-01-31T10:38:17Z")

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Dear all, I am trying to load a 4D nrrd file with size 256x256x120x20 (4D MRI data). However, it seems that the fourth dimension is not detected. The header of the file is the following: NRRD0004 # Complete NRRD file…

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## [When i use segmentedit i find a question that couldn't solve, could you help me? thank you](https://discourse.slicer.org/t/when-i-use-segmentedit-i-find-a-question-that-couldnt-solve-could-you-help-me-thank-you/21702)

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**Author:** [@wang](https://discourse.slicer.org/u/wang)\
**Replies:** 0\
**Last updated:** [January 29, 2022, 11:36pm UTC](https://discourse.slicer.org/t/when-i-use-segmentedit-i-find-a-question-that-couldnt-solve-could-you-help-me-thank-you/21702 "2022-01-29T23:36:48Z")

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I want to control the color of undo and redo, How do I get the number of operations and status of undo or redo when I use paint to edit segmentation

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## [Zoom in linked slices gets out of sync when using right-click+drag](https://discourse.slicer.org/t/zoom-in-linked-slices-gets-out-of-sync-when-using-right-click-drag/21678)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 2\
**Last updated:** [January 29, 2022, 10:19pm UTC](https://discourse.slicer.org/t/zoom-in-linked-slices-gets-out-of-sync-when-using-right-click-drag/21678 "2022-01-29T22:19:16Z")

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I linked the slice views and when I right-click+drag to change the field of view (zoom) only the field of view of the slice where my mouse is is changed. When I use ctrl+scroll all the linked slice views get synced and …

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## [Problem using Segment editor](https://discourse.slicer.org/t/problem-using-segment-editor/21689)

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**Author:** [@Keivan\_Ahmadi](https://discourse.slicer.org/u/Keivan_Ahmadi)\
**Replies:** 3\
**Last updated:** [January 29, 2022, 8:00pm UTC](https://discourse.slicer.org/t/problem-using-segment-editor/21689 "2022-01-29T20:00:11Z")

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Operating system: Windows 11 Slicer version: 4.11 Dear all, Currently, I have created a segmentation of the rat head model. I saved the following files of the segmentation for future modification. But after I load…

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## [Airway segmentation with Local Threshold (Growcut) Segment Editor Extra Effect](https://discourse.slicer.org/t/airway-segmentation-with-local-threshold-growcut-segment-editor-extra-effect/21697)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 0\
**Last updated:** [January 29, 2022, 4:48pm UTC](https://discourse.slicer.org/t/airway-segmentation-with-local-threshold-growcut-segment-editor-extra-effect/21697 "2022-01-29T16:48:03Z")

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This is the astonishing level of detail Slicer can achieve in airway segmentation (subsegmental level) with the Segment Editor Extra Effect “Local Threshold” and selection of “Growcut”. Slicer COV-19 Demo dataset (wi…

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## [about radiomic features](https://discourse.slicer.org/t/about-radiomic-features/21695)

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**Author:** [@\_Ma](https://discourse.slicer.org/u/_Ma)\
**Replies:** 0\
**Last updated:** [January 29, 2022, 4:27pm UTC](https://discourse.slicer.org/t/about-radiomic-features/21695 "2022-01-29T16:27:53Z")

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Hello,everyone, I have a question about the definition of radiomic features on the official website pyradiomics.

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## [about radiomic features](https://discourse.slicer.org/t/about-radiomic-features/21694)

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**Author:** [@Drttt](https://discourse.slicer.org/u/Drttt)\
**Replies:** 0\
**Last updated:** [January 29, 2022, 4:27pm UTC](https://discourse.slicer.org/t/about-radiomic-features/21694 "2022-01-29T16:27:47Z")

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Hello everyone, I have some questions about the definition of radiomic features on offcial website of pyradiomics. here is the sreenshots I don’t understand what p(i) means. To my understanding, p(i) is group of va…

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## [Convert unstructured grid model to volume](https://discourse.slicer.org/t/convert-unstructured-grid-model-to-volume/3867)

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**Author:** [@ghnguyen](https://discourse.slicer.org/u/ghnguyen)\
**Replies:** 4\
**Last updated:** [October 2, 2020, 12:37am UTC](https://discourse.slicer.org/t/convert-unstructured-grid-model-to-volume/3867 "2020-10-02T00:37:26Z")

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## [Segmentation exported to model file and imported does not preserve transparency](https://discourse.slicer.org/t/segmentation-exported-to-model-file-and-imported-does-not-preserve-transparency/21684)

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**Author:** [@Young\_Wang](https://discourse.slicer.org/u/Young_Wang)\
**Replies:** 1\
**Last updated:** [January 28, 2022, 11:48pm UTC](https://discourse.slicer.org/t/segmentation-exported-to-model-file-and-imported-does-not-preserve-transparency/21684 "2022-01-28T23:48:00Z")

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@lassoan maybe I am not doing this right. But I found when I export the segmentation as a model and when I reload it back and visualize it with volume rendering. It doesn’t persevere the transparency

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## [Problem using N4BiasFieldCorrection on prostate MRI](https://discourse.slicer.org/t/problem-using-n4biasfieldcorrection-on-prostate-mri/21670)

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**Author:** [@skssh](https://discourse.slicer.org/u/skssh)\
**Replies:** 2\
**Last updated:** [January 28, 2022, 11:41pm UTC](https://discourse.slicer.org/t/problem-using-n4biasfieldcorrection-on-prostate-mri/21670 "2022-01-28T23:41:34Z")

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I’m using N4BiasFieldCorrectionImageFilter from SimpleITK to adjust inhomogeneity between MR images. While the algorithm performs well on most MR images, it doesn’t perform well on some outliers. Here is an example of th…

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## [Principal components analysis in SlicerMorph](https://discourse.slicer.org/t/principal-components-analysis-in-slicermorph/21683)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 17\
**Last updated:** [January 28, 2022, 10:35pm UTC](https://discourse.slicer.org/t/principal-components-analysis-in-slicermorph/21683 "2022-01-28T22:35:50Z")

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Is there a limit to the number of points that the principal components can be calculated for using SlicerMorph? Also, if possible, could we create a method for SlicerMorph for iterative closest points in addition to the …

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## [Exporting Volume + Segmentation LabelMap as DICOM](https://discourse.slicer.org/t/exporting-volume-segmentation-labelmap-as-dicom/21648)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 10\
**Last updated:** [January 28, 2022, 11:16pm UTC](https://discourse.slicer.org/t/exporting-volume-segmentation-labelmap-as-dicom/21648 "2022-01-28T23:16:25Z")

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Hello, I am trying to export a Scalar Volume, which combines the original CT and the binary Label-Maps of the segmentation, as DICOM. Below is a coronal section of the volume and three labels, one of which is a craniopl…

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