# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=149

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

**Page:** 150

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## [Save patients ID in a list from Database with Python](https://discourse.slicer.org/t/save-patients-id-in-a-list-from-database-with-python/30872)

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**Author:** [@LisaAlborghetti](https://discourse.slicer.org/u/LisaAlborghetti)\
**Replies:** 2\
**Last updated:** [July 31, 2023, 1:37pm UTC](https://discourse.slicer.org/t/save-patients-id-in-a-list-from-database-with-python/30872 "2023-07-31T13:37:24Z")

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Hi everyone, I’m quite a new entry in the Slicer world. I’m trying to use a python script for batch conversion of structures to .vtk but I face some problems. The first issue I would like to solve is this: I loaded two …

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## [Comparing the surface changes between 2 exported mesh (.stl file or.vtk file) and showing its color map](https://discourse.slicer.org/t/comparing-the-surface-changes-between-2-exported-mesh-stl-file-or-vtk-file-and-showing-its-color-map/30881)

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**Author:** [@HNguyen](https://discourse.slicer.org/u/HNguyen)\
**Replies:** 0\
**Last updated:** [July 31, 2023, 2:29am UTC](https://discourse.slicer.org/t/comparing-the-surface-changes-between-2-exported-mesh-stl-file-or-vtk-file-and-showing-its-color-map/30881 "2023-07-31T02:29:42Z")

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Operating system: Windows 11 Slicer version: Expected behavior: Actual behavior: 5.2.2 Hello everyone, I am a new user of Slicer. I am medical student and I do not have many experiences with the software. I am invest…

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## [Make model out of binary cluster image (MRI - nifti)](https://discourse.slicer.org/t/make-model-out-of-binary-cluster-image-mri-nifti/30877)

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**Author:** [@Pia](https://discourse.slicer.org/u/Pia)\
**Replies:** 1\
**Last updated:** [July 31, 2023, 1:47am UTC](https://discourse.slicer.org/t/make-model-out-of-binary-cluster-image-mri-nifti/30877 "2023-07-31T01:47:53Z")

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Hello, I am new to 3D slicer, I would like to know if there is a way to make a 3D model out of a (binary) fmri-cluster-image I got from FSL? Thank you in advance!

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## [Slice Interpolation](https://discourse.slicer.org/t/slice-interpolation/2808)

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**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 13\
**Last updated:** [July 29, 2023, 8:25pm UTC](https://discourse.slicer.org/t/slice-interpolation/2808 "2023-07-29T20:25:15Z")

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Operating system: Windows 7 Slicer version: 4.8.1 Expected behavior: 3D Slicer should show the exact number of slices as appear in a DICOM viewer Actual behavior: 3D Slicer shows extra (and I cannot find a “match” for…

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## [Organizational Changes to DICOM Databse](https://discourse.slicer.org/t/organizational-changes-to-dicom-databse/29953)

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**Author:** [@AnishJag](https://discourse.slicer.org/u/AnishJag)\
**Replies:** 3\
**Last updated:** [July 29, 2023, 4:39pm UTC](https://discourse.slicer.org/t/organizational-changes-to-dicom-databse/29953 "2023-07-29T16:39:29Z")

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I’ve been using a custom extension for Slicer3D for bone analysis and realized that I accidentally ran an analysis on incorrect images because when importing the DICOMs from a folder, it appears extremely similar in the …

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## [Import point cloud](https://discourse.slicer.org/t/import-point-cloud/30867)

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**Author:** [@jessdtate](https://discourse.slicer.org/u/jessdtate)\
**Replies:** 1\
**Last updated:** [July 29, 2023, 3:19pm UTC](https://discourse.slicer.org/t/import-point-cloud/30867 "2023-07-29T15:19:32Z")

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I’m having trouble generalizing this solution to unstructured point clouds. I have an example text file with x, y, z values here. I can read them as an numpy array easily enough, and I noticed that there is a new Point…

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## [Model to model measurement](https://discourse.slicer.org/t/model-to-model-measurement/30866)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [July 29, 2023, 9:46am UTC](https://discourse.slicer.org/t/model-to-model-measurement/30866 "2023-07-29T09:46:38Z")

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I’m trying to measure the distance from two outer surfaces of overlapping models. this work is based on STL models without dicom. is there a way to do that ? thanks

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## [Dice dicom's image](https://discourse.slicer.org/t/dice-dicoms-image/30746)

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**Author:** [@steph85](https://discourse.slicer.org/u/steph85)\
**Replies:** 2\
**Last updated:** [July 29, 2023, 8:24am UTC](https://discourse.slicer.org/t/dice-dicoms-image/30746 "2023-07-29T08:24:12Z")

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Hello, my colleague calculate a dice with matlab with this dicom’s images, how is it possible to calculate dice on slicer 3d, i try with RT → segment comparaison but it doesn’t work. Have a nice day !

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## [Visible human project MRI dataset loading](https://discourse.slicer.org/t/visible-human-project-mri-dataset-loading/8034)

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**Author:** [@aimly](https://discourse.slicer.org/u/aimly)\
**Replies:** 15\
**Last updated:** [July 28, 2023, 9:48pm UTC](https://discourse.slicer.org/t/visible-human-project-mri-dataset-loading/8034 "2023-07-28T21:48:13Z")

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Operating system:Mac Slicer version:4.10.2 Expected behavior: Trying to load dataset from Visible human project Actual behavior: Loading problems

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## [Slicer preview build crashes when first opening extension manager](https://discourse.slicer.org/t/slicer-preview-build-crashes-when-first-opening-extension-manager/30783)

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**Author:** [@Justin\_Kirby](https://discourse.slicer.org/u/Justin_Kirby)\
**Replies:** 5\
**Last updated:** [July 28, 2023, 8:52pm UTC](https://discourse.slicer.org/t/slicer-preview-build-crashes-when-first-opening-extension-manager/30783 "2023-07-28T20:52:08Z")

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I got the following error after a fresh installation of the Preview Build (7-25) on Windows 10 when clicking “Install Extensions” on the Slicer homescreen: It crashed the program completely. I don’t see any errors in…

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## [Measurement on a plane](https://discourse.slicer.org/t/measurement-on-a-plane/30862)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 2\
**Last updated:** [July 28, 2023, 8:34pm UTC](https://discourse.slicer.org/t/measurement-on-a-plane/30862 "2023-07-28T20:34:09Z")

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is it possible to snap drawing points / measurements on a plane made in markups? if not any suggestion

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## [How to save dicom files optimized by 3D Slicer](https://discourse.slicer.org/t/how-to-save-dicom-files-optimized-by-3d-slicer/30861)

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**Author:** [@nikanika](https://discourse.slicer.org/u/nikanika)\
**Replies:** 1\
**Last updated:** [July 28, 2023, 8:26pm UTC](https://discourse.slicer.org/t/how-to-save-dicom-files-optimized-by-3d-slicer/30861 "2023-07-28T20:26:02Z")

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We found that the edge of the dicom file in 3d slcier is smoother than that of other software such as itk, and we learned that this is because 3d slcier has interpolated it. We want to export the processed image. But it …

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## [Can 3D Slicer be used for the nominal 2D picture (jpg/png etc..) label or annotation?](https://discourse.slicer.org/t/can-3d-slicer-be-used-for-the-nominal-2d-picture-jpg-png-etc-label-or-annotation/30800)

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**Author:** [@Liang\_Ma](https://discourse.slicer.org/u/Liang_Ma)\
**Replies:** 5\
**Last updated:** [July 28, 2023, 8:07pm UTC](https://discourse.slicer.org/t/can-3d-slicer-be-used-for-the-nominal-2d-picture-jpg-png-etc-label-or-annotation/30800 "2023-07-28T20:07:20Z")

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Such data (non dicom) have no meta information, so “Add DICOM Data” menu does not recognize them.

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## [How to solve loading problems in adding DICOM data](https://discourse.slicer.org/t/how-to-solve-loading-problems-in-adding-dicom-data/30864)

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**Author:** [@yumin](https://discourse.slicer.org/u/yumin)\
**Replies:** 2\
**Last updated:** [July 28, 2023, 7:37pm UTC](https://discourse.slicer.org/t/how-to-solve-loading-problems-in-adding-dicom-data/30864 "2023-07-28T19:37:22Z")

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Hi everyone! I am new to 3D slicer, and I encountered some problems in loading the data. I wonder do I need to fix the code (which I don’t know how…). It would be great if someone can help! Many thanks! Could not load: …

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## [Calibrating Ruler for JPEG Measurements](https://discourse.slicer.org/t/calibrating-ruler-for-jpeg-measurements/30818)

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**Author:** [@charlotte.jw](https://discourse.slicer.org/u/charlotte.jw)\
**Replies:** 1\
**Last updated:** [July 28, 2023, 2:50pm UTC](https://discourse.slicer.org/t/calibrating-ruler-for-jpeg-measurements/30818 "2023-07-28T14:50:05Z")

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Hi there, I’m completely new to slicer and need a very simple distance measurement from the program but am unsure how to do so. I will be uploading JPEG images of cadaveric specimens with a ruler in the photo for scale.…

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## [Using a scaled down version of a volume to segment, then using this segment on original large size volumes](https://discourse.slicer.org/t/using-a-scaled-down-version-of-a-volume-to-segment-then-using-this-segment-on-original-large-size-volumes/30853)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 2\
**Last updated:** [July 28, 2023, 2:17pm UTC](https://discourse.slicer.org/t/using-a-scaled-down-version-of-a-volume-to-segment-then-using-this-segment-on-original-large-size-volumes/30853 "2023-07-28T14:17:11Z")

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Dear all, I have large datasets (10 to 30GB per image) which are thus difficult to segment on original files. One solution I imagined is 1- to use a 10X downscaled version of my images, 2- paint “seeds” in the 14 reg…

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## [I need to do diffusion and tractography with 3D slicer from the resonance images. Can someone tell me if it is possible and if it is, I would appreciate a link to a tutorial. Thank you!!](https://discourse.slicer.org/t/i-need-to-do-diffusion-and-tractography-with-3d-slicer-from-the-resonance-images-can-someone-tell-me-if-it-is-possible-and-if-it-is-i-would-appreciate-a-link-to-a-tutorial-thank-you/30838)

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**Author:** [@Carlos\_Lujan](https://discourse.slicer.org/u/Carlos_Lujan)\
**Replies:** 2\
**Last updated:** [July 28, 2023, 1:47pm UTC](https://discourse.slicer.org/t/i-need-to-do-diffusion-and-tractography-with-3d-slicer-from-the-resonance-images-can-someone-tell-me-if-it-is-possible-and-if-it-is-i-would-appreciate-a-link-to-a-tutorial-thank-you/30838 "2023-07-28T13:47:03Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Cardiac CT and CMR postprocessing](https://discourse.slicer.org/t/cardiac-ct-and-cmr-postprocessing/30222)

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**Author:** [@Villurca](https://discourse.slicer.org/u/Villurca)\
**Replies:** 4\
**Last updated:** [July 28, 2023, 1:12pm UTC](https://discourse.slicer.org/t/cardiac-ct-and-cmr-postprocessing/30222 "2023-07-28T13:12:25Z")

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\<I need to CPR coronary arteries for evaluation grade stenosis Agatson coronay score and 3D VRI. In VR the tools no working (scissors and so on) with python console filling a lot of error of any tool. I want to know how …

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## [Problem with data bases ](https://discourse.slicer.org/t/problem-with-data-bases/30840)

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**Author:** [@Mcgiler](https://discourse.slicer.org/u/Mcgiler)\
**Replies:** 2\
**Last updated:** [July 28, 2023, 11:49am UTC](https://discourse.slicer.org/t/problem-with-data-bases/30840 "2023-07-28T11:49:16Z")

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Hi, Lately I changed the location of the DICOM files on my computer. Since then I’m not able to load patients because the file path is not existing. I was trying to remove the patients from the the DICOM database (by r…

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## [Wiki account creation](https://discourse.slicer.org/t/wiki-account-creation/30837)

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**Author:** [@SL2027](https://discourse.slicer.org/u/SL2027)\
**Replies:** 1\
**Last updated:** [July 28, 2023, 1:26am UTC](https://discourse.slicer.org/t/wiki-account-creation/30837 "2023-07-28T01:26:15Z")

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Hello, I have been working on the TCIA Browser extension for the past couple of weeks, and I would like to update the wiki page for the extension. I requested an account, but I have not received the confirmation email ye…

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## [Automatic centerline generation and post processing steps](https://discourse.slicer.org/t/automatic-centerline-generation-and-post-processing-steps/30841)

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**Author:** [@Ali\_Mokhtari](https://discourse.slicer.org/u/Ali_Mokhtari)\
**Replies:** 0\
**Last updated:** [July 28, 2023, 1:17am UTC](https://discourse.slicer.org/t/automatic-centerline-generation-and-post-processing-steps/30841 "2023-07-28T01:17:55Z")

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Hi all, I have a stl file for a bifurcation case (along the Z axis). I want to generate the centerline for this geometry. In the next step, I want to create the boundary planes perpendicular to this centerline (on the …

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## [Cardiac modules not available despite installing the Slicer Heart extension ](https://discourse.slicer.org/t/cardiac-modules-not-available-despite-installing-the-slicer-heart-extension/30839)

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**Author:** [@Doaa\_Mahgoub](https://discourse.slicer.org/u/Doaa_Mahgoub)\
**Replies:** 0\
**Last updated:** [July 28, 2023, 1:16am UTC](https://discourse.slicer.org/t/cardiac-modules-not-available-despite-installing-the-slicer-heart-extension/30839 "2023-07-28T01:16:01Z")

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I installed the Slicer Heart (by downloading it to my PC from the extension catalog website then installing it from my PC to the Slicer 5.2.2), however, I cannot find any of the cardiac modules in the modules drop list. …

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## [Get the same array size after transform](https://discourse.slicer.org/t/get-the-same-array-size-after-transform/30782)

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**Author:** [@Jakub\_Mitura](https://discourse.slicer.org/u/Jakub_Mitura)\
**Replies:** 1\
**Last updated:** [July 27, 2023, 5:54pm UTC](https://discourse.slicer.org/t/get-the-same-array-size-after-transform/30782 "2023-07-27T17:54:11Z")

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Hello, I use Fiducial registration to obtain linear transform. I saved markup points, transform, original 3d images, and transformed 3d image (checked apply transform when saving file). After applying this transform, im…

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## [Import point cloud data](https://discourse.slicer.org/t/import-point-cloud-data/1382)

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**Author:** [@Hamburgerfinger](https://discourse.slicer.org/u/Hamburgerfinger)\
**Replies:** 17\
**Last updated:** [November 8, 2017, 10:31pm UTC](https://discourse.slicer.org/t/import-point-cloud-data/1382 "2017-11-08T22:31:18Z")

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I have image data in point cloud format (4 columns: x,y,z,intensity). How can I import this volume, or convert it to a format I can import into Slicer? Any help would be most appreciated!

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## [Segmentation (.seg.nrrd) merges labels instead of one-layer-per-label representation](https://discourse.slicer.org/t/segmentation-seg-nrrd-merges-labels-instead-of-one-layer-per-label-representation/30792)

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**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 1\
**Last updated:** [July 27, 2023, 4:25pm UTC](https://discourse.slicer.org/t/segmentation-seg-nrrd-merges-labels-instead-of-one-layer-per-label-representation/30792 "2023-07-27T16:25:23Z")

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Hi, I have noticed that the array in the saved segmentation file (.seg.nrrd) is not really one-layer-per-label. Instead, non-overlapping labels are merged into one layer, while overlapping layers are kept separately. I…

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## [Multi-threading for paint and grow from seeds](https://discourse.slicer.org/t/multi-threading-for-paint-and-grow-from-seeds/30802)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 3\
**Last updated:** [July 27, 2023, 2:50pm UTC](https://discourse.slicer.org/t/multi-threading-for-paint-and-grow-from-seeds/30802 "2023-07-27T14:50:08Z")

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Dear all, We run slicer on a linux calculation server because our 3D datasets are large (~50 GB per image). I’ve seen a couple of posts and detailed answers about multi-threading but can i ask you if “paint” and “grow …

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## [Default location of volumes data and files](https://discourse.slicer.org/t/default-location-of-volumes-data-and-files/30831)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 0\
**Last updated:** [July 27, 2023, 2:46pm UTC](https://discourse.slicer.org/t/default-location-of-volumes-data-and-files/30831 "2023-07-27T14:46:42Z")

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Dear all, I’m on the latest linux build and I can t find a way to let slicer know by default the location of data files. Is this possible somehow (can t find anywhere in application settings or in SlicerLauncherSettnigs…

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## [An extension for creating signal intensity histogram](https://discourse.slicer.org/t/an-extension-for-creating-signal-intensity-histogram/30824)

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**Author:** [@Shadi\_Afyouni](https://discourse.slicer.org/u/Shadi_Afyouni)\
**Replies:** 0\
**Last updated:** [July 27, 2023, 12:20am UTC](https://discourse.slicer.org/t/an-extension-for-creating-signal-intensity-histogram/30824 "2023-07-27T00:20:13Z")

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When would you add an extension which creates a voxel intensity histogram or an extension that gives us the voxel values?

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## [Save and import ROI for multiple MRI series](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30822)

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**Author:** [@EduardVerheijen](https://discourse.slicer.org/u/EduardVerheijen)\
**Replies:** 0\
**Last updated:** [July 27, 2023, 12:19am UTC](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30822 "2023-07-27T00:19:45Z")

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Hi all, I am new to using 3D slicer. For a project I want to crop a 400x400 pixel ROI box from axial MRI scans and export them as DICOM. I managed to do it for one patient’s MRI series, but I need to have the exact same…

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## [Cannot Import DICOM files](https://discourse.slicer.org/t/cannot-import-dicom-files/30821)

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**Author:** [@Warren\_Rosengren](https://discourse.slicer.org/u/Warren_Rosengren)\
**Replies:** 0\
**Last updated:** [July 27, 2023, 12:18am UTC](https://discourse.slicer.org/t/cannot-import-dicom-files/30821 "2023-07-27T00:18:38Z")

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I am trying to import a DICOM file so I can turn it into a NRRD file to convert to a STL. When I attempt to add the DICOM folder I get this error W: DcmSequenceOfItems: Reached end of stream before the end of sequence P…

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