# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=55

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

**Page:** 56

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## [Endocranial volume in 3D Slicer](https://discourse.slicer.org/t/endocranial-volume-in-3d-slicer/41239)

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**Author:** [@ThomasVanParys](https://discourse.slicer.org/u/ThomasVanParys)\
**Replies:** 5\
**Last updated:** [January 28, 2025, 3:34pm UTC](https://discourse.slicer.org/t/endocranial-volume-in-3d-slicer/41239 "2025-01-28T15:34:12Z")

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Hello, I am segmenting skulls from the NDMDID PM-CT dataset. I want to measure endocranial volume, or some measure of cranial capacity/brain size. What is best or easiest way to do this from the skull models? Here is …

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## [Placing Landmarks on 2D images](https://discourse.slicer.org/t/placing-landmarks-on-2d-images/41337)

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**Author:** [@Kowsar\_Sheikhi](https://discourse.slicer.org/u/Kowsar_Sheikhi)\
**Replies:** 1\
**Last updated:** [January 28, 2025, 2:27pm UTC](https://discourse.slicer.org/t/placing-landmarks-on-2d-images/41337 "2025-01-28T14:27:17Z")

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How can I accurately place landmarks on 2D CT and MRI images of the knee? I have used the Markups tool before, but I’m not sure if I did it correctly. Could anyone guide me through the process of placing landmarks using…

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## [Threshold does not work when saved data loaded again](https://discourse.slicer.org/t/threshold-does-not-work-when-saved-data-loaded-again/37376)

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**Author:** [@Figaya](https://discourse.slicer.org/u/Figaya)\
**Replies:** 3\
**Last updated:** [January 27, 2025, 9:18pm UTC](https://discourse.slicer.org/t/threshold-does-not-work-when-saved-data-loaded-again/37376 "2025-01-27T21:18:22Z")

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Hello, The threshold does not apply when I perform the following steps: Load MRHead sample data. Go to the Segment Editor module. Add a segment. Open the Threshold effect (DO NOT APPLY THE THRESHOLD NOW). Press CTRL+S…

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## [Cannot start\_server for MONAILABEL](https://discourse.slicer.org/t/cannot-start-server-for-monailabel/27406)

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**Author:** [@Bor\_Antolic](https://discourse.slicer.org/u/Bor_Antolic)\
**Replies:** 3\
**Last updated:** [January 27, 2025, 6:11pm UTC](https://discourse.slicer.org/t/cannot-start-server-for-monailabel/27406 "2025-01-27T18:11:27Z")

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Hi! I hope someone could help me with my problem. I successfully installed Monailabel on my home (Mac)computer, started the server, and it works inside 3D Slicer. I followed same steps to install it on my work Windows co…

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## [Can't access MONAI Label server from 3D Slicer](https://discourse.slicer.org/t/cant-access-monai-label-server-from-3d-slicer/31301)

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**Author:** [@shihje](https://discourse.slicer.org/u/shihje)\
**Replies:** 11\
**Last updated:** [January 27, 2025, 6:10pm UTC](https://discourse.slicer.org/t/cant-access-monai-label-server-from-3d-slicer/31301 "2025-01-27T18:10:35Z")

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I’m trying to use 3D Slicer as a visualization tool for MONAI Label. I started up the MONAI Label server using the monailabel CLI in an SSH terminal, and got an IP address of the Uvicorn session: I then input this IP…

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## [Issue while starting the MONAILabel server](https://discourse.slicer.org/t/issue-while-starting-the-monailabel-server/25839)

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**Author:** [@deboshree\_roy](https://discourse.slicer.org/u/deboshree_roy)\
**Replies:** 2\
**Last updated:** [January 27, 2025, 6:09pm UTC](https://discourse.slicer.org/t/issue-while-starting-the-monailabel-server/25839 "2025-01-27T18:09:30Z")

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Problem report for Slicer 5.0.3 win-amd64: \[please describe expected and actual behavior\] While initializing the server an error message - \[2022-10-22 12:03:10,941\] \[2356\] \[MainThread\] \[INFO\] (uvicorn.error:59) - Appli…

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## [Magneticencephalography(MEG) for neuro-imaging fif files supportive in 3D slicer 5.0version](https://discourse.slicer.org/t/magneticencephalography-meg-for-neuro-imaging-fif-files-supportive-in-3d-slicer-5-0version/41311)

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**Author:** [@Sri](https://discourse.slicer.org/u/Sri)\
**Replies:** 0\
**Last updated:** [January 27, 2025, 12:15pm UTC](https://discourse.slicer.org/t/magneticencephalography-meg-for-neuro-imaging-fif-files-supportive-in-3d-slicer-5-0version/41311 "2025-01-27T12:15:25Z")

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i have a project which combines MEG files and MRI and PET files together does 3D slicer support fif files also?

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## [Convert DICOM-RTSTRUCT format to Nifti format](https://discourse.slicer.org/t/convert-dicom-rtstruct-format-to-nifti-format/1580)

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**Author:** [@glhfgg1024](https://discourse.slicer.org/u/glhfgg1024)\
**Replies:** 10\
**Last updated:** [January 27, 2025, 7:02am UTC](https://discourse.slicer.org/t/convert-dicom-rtstruct-format-to-nifti-format/1580 "2025-01-27T07:02:41Z")

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Hi all, I’m facing another problem. I’m using machine learning method to do segmentation for medical images, and at first I convert the DICOM files to Nifti format. I have several DICOM directories and their correspondin…

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## [The LV model reconstruction of 2D cineMRI](https://discourse.slicer.org/t/the-lv-model-reconstruction-of-2d-cinemri/41301)

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**Author:** [@LWRwada](https://discourse.slicer.org/u/LWRwada)\
**Replies:** 0\
**Last updated:** [January 27, 2025, 2:21am UTC](https://discourse.slicer.org/t/the-lv-model-reconstruction-of-2d-cinemri/41301 "2025-01-27T02:21:50Z")

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Hi, Everyone! Recently, I have acquired 2D cine MRI data. For the sagittal and short-axis planes, the cine series contains 20 frames per plane. I have already created the LV model at the ED phase. I would like to recon…

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## [bad\_alloc error in slicerfreesurfer on 5.2.1 Linux](https://discourse.slicer.org/t/bad-alloc-error-in-slicerfreesurfer-on-5-2-1-linux/26694)

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**Author:** [@kytk](https://discourse.slicer.org/u/kytk)\
**Replies:** 6\
**Last updated:** [January 26, 2025, 10:11pm UTC](https://discourse.slicer.org/t/bad-alloc-error-in-slicerfreesurfer-on-5-2-1-linux/26694 "2025-01-26T22:11:12Z")

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Hi, I have trouble using FreeSurfer Importer provided with the SlicerFreSurfer extension. Problem: When I try to load segmentation, it cuases bad\_alloc error. The error message is below. “Slicer has caught an applicat…

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## [Getting longest dimension of surface mesh with SVD](https://discourse.slicer.org/t/getting-longest-dimension-of-surface-mesh-with-svd/40694)

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**Author:** [@evaherbst](https://discourse.slicer.org/u/evaherbst)\
**Replies:** 3\
**Last updated:** [January 26, 2025, 6:12pm UTC](https://discourse.slicer.org/t/getting-longest-dimension-of-surface-mesh-with-svd/40694 "2025-01-26T18:12:55Z")

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Hello, I am working with vtk and np.linalg.svd to get the main axes of a surface mesh. I want to use the SVD singular values to find the longest dimensions of the model (as far as I understand, the singular values repr…

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## [Shortcut keys doesnt work properly on Dental Segmentator 3dSlicer 5.8.0](https://discourse.slicer.org/t/shortcut-keys-doesnt-work-properly-on-dental-segmentator-3dslicer-5-8-0/41286)

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**Author:** [@Esteban\_Barreiro](https://discourse.slicer.org/u/Esteban_Barreiro)\
**Replies:** 2\
**Last updated:** [January 25, 2025, 7:11pm UTC](https://discourse.slicer.org/t/shortcut-keys-doesnt-work-properly-on-dental-segmentator-3dslicer-5-8-0/41286 "2025-01-25T19:11:45Z")

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Hi there! Im using 3dSlicer 5.8.0 and the shortcut ESC doesnt work properly on Dental Segmentator, it does not cancel the editing effect as in the Segment Editor Extra Effects. Also you cant change the name of the segm…

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## [How can I download interactive charting of sequence module :(](https://discourse.slicer.org/t/how-can-i-download-interactive-charting-of-sequence-module/41277)

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**Author:** [@yuriel](https://discourse.slicer.org/u/yuriel)\
**Replies:** 0\
**Last updated:** [January 25, 2025, 10:54am UTC](https://discourse.slicer.org/t/how-can-i-download-interactive-charting-of-sequence-module/41277 "2025-01-25T10:54:06Z")

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Hi! I’m newbie in 3D Slicer. I want to measure difference between the FLAIR sequences signal intensity but I only can find the interactive charting in Sequence module. Can I get a numeric values for this charting?

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## [3d Slicer and Amira have different(opposite) orientation](https://discourse.slicer.org/t/3d-slicer-and-amira-have-different-opposite-orientation/41245)

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**Author:** [@Puja\_Ghosh](https://discourse.slicer.org/u/Puja_Ghosh)\
**Replies:** 12\
**Last updated:** [January 24, 2025, 9:17pm UTC](https://discourse.slicer.org/t/3d-slicer-and-amira-have-different-opposite-orientation/41245 "2025-01-24T21:17:29Z")

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Why MRI data orientation of 3d Slicer and Amira is opposite? the left and right side is opposite to each other? Can anyone please tell why this happens? which one is correct?

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## [A bit of confusion about the slicer coordinate system](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883)

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**Author:** [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Replies:** 13\
**Last updated:** [January 24, 2025, 8:54pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883 "2025-01-24T20:54:55Z")

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The itk coordinate system is lps, and the slider is ras. However, why does the cursor on the slider display coordinates that are not actually ras? For example, the dicom coordinates are (1, 1, 1), while the actual coordi…

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## [Creating fibular cutting guide and saved data](https://discourse.slicer.org/t/creating-fibular-cutting-guide-and-saved-data/41208)

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**Author:** [@Enkh-Orchlon\_Batbaya](https://discourse.slicer.org/u/Enkh-Orchlon_Batbaya)\
**Replies:** 4\
**Last updated:** [January 24, 2025, 6:11pm UTC](https://discourse.slicer.org/t/creating-fibular-cutting-guide-and-saved-data/41208 "2025-01-24T18:11:55Z")

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Dear All, I have working on this case couple days, and finally able to plan fibula cutiing guide. However, after creating the guide using boolean operation and saved it as STL file, I could not see any miter box and hol…

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## [DentalSegmentator error](https://discourse.slicer.org/t/dentalsegmentator-error/41262)

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**Author:** [@Nermin\_Morgan](https://discourse.slicer.org/u/Nermin_Morgan)\
**Replies:** 0\
**Last updated:** [January 24, 2025, 3:32pm UTC](https://discourse.slicer.org/t/dentalsegmentator-error/41262 "2025-01-24T15:32:47Z")

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Hello I downloaded preview version 5.7 and I could not use the dental segmentator, this error appears in the console: \[Qt\] void \_\_cdecl qMRMLSegmentEditorWidget::setSourceVolumeNode(class vtkMRMLNode \*) failed: need t…

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## [DICOM Files not displaying different views properly](https://discourse.slicer.org/t/dicom-files-not-displaying-different-views-properly/41261)

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**Author:** [@sofia](https://discourse.slicer.org/u/sofia)\
**Replies:** 1\
**Last updated:** [January 24, 2025, 3:31pm UTC](https://discourse.slicer.org/t/dicom-files-not-displaying-different-views-properly/41261 "2025-01-24T15:31:57Z")

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I am relatively new to using slicer, I have only used tutorial sets of data, which are automatically set up to open all views properly. My issue, however, is that when opening, nothing looks right, and I don’t know ho…

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## [Importing Color-Corrected TIFFs](https://discourse.slicer.org/t/importing-color-corrected-tiffs/41260)

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**Author:** [@milbelle](https://discourse.slicer.org/u/milbelle)\
**Replies:** 0\
**Last updated:** [January 24, 2025, 3:27pm UTC](https://discourse.slicer.org/t/importing-color-corrected-tiffs/41260 "2025-01-24T15:27:29Z")

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Hello! Hope you’re all having a lovely January so far. I recently received a scan that I needed to do some color correcting to, in order to increase contrast. I have done so in Lightroom since that is the program that i…

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## [Gantry rotation order?](https://discourse.slicer.org/t/gantry-rotation-order/41259)

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**Author:** [@DeclanGarvey](https://discourse.slicer.org/u/DeclanGarvey)\
**Replies:** 0\
**Last updated:** [January 24, 2025, 3:26pm UTC](https://discourse.slicer.org/t/gantry-rotation-order/41259 "2025-01-24T15:26:19Z")

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Hi, I am currently writing my own code for coordinate transformations which will involve Gantry rotation around Y and Gantry pitch rotation around X. So I was wondering what is the standard order of rotations, is it pitc…

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## [3d view in segmentation rendering does not show anyting](https://discourse.slicer.org/t/3d-view-in-segmentation-rendering-does-not-show-anyting/41254)

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**Author:** [@alex\_He](https://discourse.slicer.org/u/alex_He)\
**Replies:** 3\
**Last updated:** [January 24, 2025, 2:26pm UTC](https://discourse.slicer.org/t/3d-view-in-segmentation-rendering-does-not-show-anyting/41254 "2025-01-24T14:26:05Z")

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hi I tried to show the 3d view in the volume rendering module but unsucessful. please advise and see the attached screen capture. thank you

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## [Can't download because the source file cannot be read](https://discourse.slicer.org/t/cant-download-because-the-source-file-cannot-be-read/41158)

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**Author:** [@ValerieS](https://discourse.slicer.org/u/ValerieS)\
**Replies:** 16\
**Last updated:** [January 23, 2025, 10:58pm UTC](https://discourse.slicer.org/t/cant-download-because-the-source-file-cannot-be-read/41158 "2025-01-23T22:58:30Z")

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I’m working on Windows 11, can’t download 5.6.2. It gets to about 15% and then stops. I get a message saying ‘can’t download because the source file cannot be read’. I have not used 3D slicer for a while, but the 4.10.2 …

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## [TAVR module in Slicer](https://discourse.slicer.org/t/tavr-module-in-slicer/41171)

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**Author:** [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Replies:** 1\
**Last updated:** [January 23, 2025, 3:37pm UTC](https://discourse.slicer.org/t/tavr-module-in-slicer/41171 "2025-01-23T15:37:14Z")

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Hi all, I saw this video and I was wondering which extension/module is that (and how to get it). Any idea? Thanks a lot. Paolo

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## [Need help on changing dicom modality](https://discourse.slicer.org/t/need-help-on-changing-dicom-modality/41212)

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**Author:** [@alientex](https://discourse.slicer.org/u/alientex)\
**Replies:** 3\
**Last updated:** [January 23, 2025, 1:29pm UTC](https://discourse.slicer.org/t/need-help-on-changing-dicom-modality/41212 "2025-01-23T13:29:06Z")

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Hello, As per my use case, I want to change the modality of DICOM data when importing a DICOM directory, so that when viewing the DICOM metadata, it reflects the changes I made. Can anyone please help me achieve thi…

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## [Easy way to display the metadata of a CT](https://discourse.slicer.org/t/easy-way-to-display-the-metadata-of-a-ct/41220)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 1\
**Last updated:** [January 23, 2025, 1:13pm UTC](https://discourse.slicer.org/t/easy-way-to-display-the-metadata-of-a-ct/41220 "2025-01-23T13:13:45Z")

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Hello, I’m working on cases transfered by an hospital. The case contains multiple CT. When I load the CT they are ordered by the series number. I want to order them by acquisition time to make it easier to understand th…

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## [Export DICOM-SEG data](https://discourse.slicer.org/t/export-dicom-seg-data/21636)

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**Author:** [@Johannes](https://discourse.slicer.org/u/Johannes)\
**Replies:** 4\
**Last updated:** [January 23, 2025, 11:33am UTC](https://discourse.slicer.org/t/export-dicom-seg-data/21636 "2025-01-23T11:33:16Z")

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Hi everyone, I cannot export DICOM SEG files from anonymized DICOM files. It works without any problems with DICOM objects that have not been anonymized. As an example, this dataset from the internet can be used to re…

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## [Segment section of adipose tissue whose radial distance from the blood vessel wall is equal to the diameter of the blood vessel.](https://discourse.slicer.org/t/segment-section-of-adipose-tissue-whose-radial-distance-from-the-blood-vessel-wall-is-equal-to-the-diameter-of-the-blood-vessel/41017)

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**Author:** [@seraphina](https://discourse.slicer.org/u/seraphina)\
**Replies:** 15\
**Last updated:** [January 23, 2025, 8:39am UTC](https://discourse.slicer.org/t/segment-section-of-adipose-tissue-whose-radial-distance-from-the-blood-vessel-wall-is-equal-to-the-diameter-of-the-blood-vessel/41017 "2025-01-23T08:39:58Z")

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I would like to obtain a segment of adipose tissue whose radial distance from the blood vessel wall is equal to the diameter of the blood vessel, and this segment can change along with the variation of the blood vessel d…

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## [Constraining ruler tool to a perfectly horizontal or vertical line](https://discourse.slicer.org/t/constraining-ruler-tool-to-a-perfectly-horizontal-or-vertical-line/41229)

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**Author:** [@Bella\_Salerno](https://discourse.slicer.org/u/Bella_Salerno)\
**Replies:** 0\
**Last updated:** [January 22, 2025, 7:17pm UTC](https://discourse.slicer.org/t/constraining-ruler-tool-to-a-perfectly-horizontal-or-vertical-line/41229 "2025-01-22T19:17:51Z")

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Hello, I have a question regarding the ruler tool and creating a measurement line. Is there a way to ‘snap’ the line to a perfectly horizontal or vertical line? For example, in other applications I can hold down the “sh…

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## [How to Improve TotalSegmentator's Spine Segmentation in 3D Slicer?](https://discourse.slicer.org/t/how-to-improve-totalsegmentators-spine-segmentation-in-3d-slicer/41213)

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**Author:** [@wenlin\_x](https://discourse.slicer.org/u/wenlin_x)\
**Replies:** 1\
**Last updated:** [January 22, 2025, 7:09pm UTC](https://discourse.slicer.org/t/how-to-improve-totalsegmentators-spine-segmentation-in-3d-slicer/41213 "2025-01-22T19:09:17Z")

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Hi, I am using TotalSegmentator to segment the spine from CT scans. However, I noticed that certain parts, such as the spinous processes, are not segmented very well. I would like to manually refine the segmentation res…

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## [Empty voxels upon joint smoothing](https://discourse.slicer.org/t/empty-voxels-upon-joint-smoothing/41194)

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**Author:** [@coco](https://discourse.slicer.org/u/coco)\
**Replies:** 6\
**Last updated:** [January 22, 2025, 4:05pm UTC](https://discourse.slicer.org/t/empty-voxels-upon-joint-smoothing/41194 "2025-01-22T16:05:21Z")

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Dear all, We have brain samples that we segment using a seeding/grow from seeds approach followed by a joint smoothing. This last step results in a couple of empty voxels as you can see on the picture below: the red…

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