# \#brain

**URL:** https://discourse.slicer.org/tag/brain/46.md

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

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## [Overlay of coregistered brain MRI and CT](https://discourse.slicer.org/t/overlay-of-coregistered-brain-mri-and-ct/35465)

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**Author:** [@Kerezoudis](https://discourse.slicer.org/u/Kerezoudis)\
**Replies:** 2\
**Last updated:** [July 8, 2026, 8:53am UTC](https://discourse.slicer.org/t/overlay-of-coregistered-brain-mri-and-ct/35465 "2026-07-08T08:53:44Z")

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Operating system: MacOs Sonoma 14.4.1 Slicer version: 5.6.1 Expected behavior: I would like to overlay preoperative brain MRI with postoperative CT (after electrode placement) Actual behavior: images are not aligned. …

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## [Which is the best extension for Brain parcellation?](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483)

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**Author:** [@Suhaim](https://discourse.slicer.org/u/Suhaim)\
**Replies:** 3\
**Last updated:** [June 11, 2026, 9:28pm UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483 "2026-06-11T21:28:16Z")

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Hi, Is there any extension in 3D-Slicer which offers automated brain segmentation for parts such as - Amygdala, Hippocampus, Insula etc.? Which extension has the best accuracy? I was able to find SlicerNeuroSegmentatio…

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## [Segmenting individual lobes in an abnormal brain (with hydrocephalus)](https://discourse.slicer.org/t/segmenting-individual-lobes-in-an-abnormal-brain-with-hydrocephalus/47275)

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**Author:** [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Replies:** 6\
**Last updated:** [June 8, 2026, 8:35pm UTC](https://discourse.slicer.org/t/segmenting-individual-lobes-in-an-abnormal-brain-with-hydrocephalus/47275 "2026-06-08T20:35:50Z")

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Hello everyone, I am currently working on hydrocephalus . I need do segment the lobes of the brain in MRI of children with hydrocephalus . I saw a few extensions on 3D slicer and some sites like VolBrain but they are on…

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## [SwissSkullStripper is having trouble with multiple splices, and so am I](https://discourse.slicer.org/t/swissskullstripper-is-having-trouble-with-multiple-splices-and-so-am-i/47111)

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**Author:** [@HomerHaddock](https://discourse.slicer.org/u/HomerHaddock)\
**Replies:** 0\
**Last updated:** [May 21, 2026, 8:30pm UTC](https://discourse.slicer.org/t/swissskullstripper-is-having-trouble-with-multiple-splices-and-so-am-i/47111 "2026-05-21T20:30:45Z")

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I am having trouble with getting a CT scan exported. The scan has one splice for X, Y, and Z where it gets the most quality. To show my problem I used the scan best used on the horizontal plane (It has the most imaging…

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## [Brain Modelling](https://discourse.slicer.org/t/brain-modelling/46154)

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**Author:** [@nakcali](https://discourse.slicer.org/u/nakcali)\
**Replies:** 2\
**Last updated:** [February 14, 2026, 3:36pm UTC](https://discourse.slicer.org/t/brain-modelling/46154 "2026-02-14T15:36:52Z")

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Hello, Can someone help me? I am trying to create a 3D model of my brain. I am using Swiss Skull Stripper, but I am not able to do it properly. It looks like lego brain. My MRI data seem to be divided into several grou…

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## [Brain Modelling from MRI images // Help](https://discourse.slicer.org/t/brain-modelling-from-mri-images-help/45841)

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**Author:** [@nakcali](https://discourse.slicer.org/u/nakcali)\
**Replies:** 0\
**Last updated:** [January 20, 2026, 2:35pm UTC](https://discourse.slicer.org/t/brain-modelling-from-mri-images-help/45841 "2026-01-20T14:35:59Z")

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Hello, I am trying to create a 3D model of my brain. I am using Swiss Skull Stripper, but I am not able to do it properly. It looks like lego brain. My MRI data seem to be divided into several groups (for example: right…

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## [A thank you from a novice user and motivated brain cancer patient](https://discourse.slicer.org/t/a-thank-you-from-a-novice-user-and-motivated-brain-cancer-patient/44559)

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**Author:** [@OligoStu](https://discourse.slicer.org/u/OligoStu)\
**Replies:** 1\
**Last updated:** [September 23, 2025, 12:40pm UTC](https://discourse.slicer.org/t/a-thank-you-from-a-novice-user-and-motivated-brain-cancer-patient/44559 "2025-09-23T12:40:40Z")

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I’m writing a note of thanks to the developers and community after having found 3D slicer earlier this year and learning how to use it to get a fuller understanding from my routine MRIs to track progress of my brain tumo…

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## [Slicer doesn't open after installing SlicerWMA extension](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356)

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**Author:** [@Dmytro\_Shyshlov](https://discourse.slicer.org/u/Dmytro_Shyshlov)\
**Replies:** 5\
**Last updated:** [April 3, 2025, 12:44am UTC](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356 "2025-04-03T00:44:42Z")

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Hello! I’m trying to run Slicer 5.8.1 on CentOS 7.9 server with 3 extensions: SlicerDMRI, SlicerWMA, UKFTractography. Everything works fine with DMRI and UKFT, but every time I try to install SlicerWMA the program doesn…

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## [Converting 2d hand drawn atlas into 3d atlas with region volumes](https://discourse.slicer.org/t/converting-2d-hand-drawn-atlas-into-3d-atlas-with-region-volumes/41920)

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**Author:** [@imillercrews](https://discourse.slicer.org/u/imillercrews)\
**Replies:** 2\
**Last updated:** [March 3, 2025, 1:58pm UTC](https://discourse.slicer.org/t/converting-2d-hand-drawn-atlas-into-3d-atlas-with-region-volumes/41920 "2025-03-03T13:58:37Z")

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My field uses an old hand drawn bird brain atlas from the 70’s for doing dissections and I wanted to try and convert the 2d images into a 3d model for demonstration and training purposes. Does this seem like something 3D…

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## [Export Brainstorm seeg coordinates to 3D Slicer](https://discourse.slicer.org/t/export-brainstorm-seeg-coordinates-to-3d-slicer/40986)

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**Author:** [@stephanejean](https://discourse.slicer.org/u/stephanejean)\
**Replies:** 5\
**Last updated:** [January 8, 2025, 3:57am UTC](https://discourse.slicer.org/t/export-brainstorm-seeg-coordinates-to-3d-slicer/40986 "2025-01-08T03:57:11Z")

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Hello, I have been using 3D slicer for a while now, I would like to export SEEG contact location generate to brainstorm into 3D slicer and convert each contacts into a segment sphere using the xyz coordinates. Is it poss…

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## [Segmentation the hippocampus automatically](https://discourse.slicer.org/t/segmentation-the-hippocampus-automatically/40929)

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**Author:** [@mtekeli](https://discourse.slicer.org/u/mtekeli)\
**Replies:** 1\
**Last updated:** [January 2, 2025, 2:59pm UTC](https://discourse.slicer.org/t/segmentation-the-hippocampus-automatically/40929 "2025-01-02T14:59:46Z")

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greetings to everyone i am working on segmentation the hippocampus automatically. i tried a few plugins like Raidionics, Slicerneuro but i couldn’t do it. is there a method you can suggest?

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## [Why does my HD Brain Extration Tool fail to computing?](https://discourse.slicer.org/t/why-does-my-hd-brain-extration-tool-fail-to-computing/40627)

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**Author:** [@researchtomliu](https://discourse.slicer.org/u/researchtomliu)\
**Replies:** 2\
**Last updated:** [December 14, 2024, 1:34am UTC](https://discourse.slicer.org/t/why-does-my-hd-brain-extration-tool-fail-to-computing/40627 "2024-12-14T01:34:19Z")

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Hello, I have updated the Slicer to the latest version 5.7. When I used the model “HD Brain Extration Tool”, It could not comptue and gave some error warnning masages. How to solve it? Thanks! Traceback (most recent cal…

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## [How to do and negative brain segmentation](https://discourse.slicer.org/t/how-to-do-and-negative-brain-segmentation/40366)

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**Author:** [@Victor\_Hugo\_Figueire](https://discourse.slicer.org/u/Victor_Hugo_Figueire)\
**Replies:** 0\
**Last updated:** [November 25, 2024, 2:27pm UTC](https://discourse.slicer.org/t/how-to-do-and-negative-brain-segmentation/40366 "2024-11-25T14:27:24Z")

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Hello!, I am trying to find and easy way to do this structure : a block with the brain volume on negative , similar to this article approach .

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## [How to create a brain mask from MRI T2 (30 MRI total)](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338)

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**Author:** [@jegiron](https://discourse.slicer.org/u/jegiron)\
**Replies:** 3\
**Last updated:** [September 13, 2024, 7:36pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338 "2024-09-13T19:36:55Z")

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I have MRI T2 weighed images and need to create a mask to remove skull and others. I have a total of 30 MRI models and need ultimately need to measure infarct volume percentage. I also need to do spatial normalization. H…

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## [Brain Segmentation in MR](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924)

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**Author:** [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Replies:** 5\
**Last updated:** [July 19, 2024, 7:00pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924 "2024-07-19T19:00:19Z")

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Operating system: Windows Slicer version:5.6.2 Expected behavior: I have been trying to get a good brain segmentation for quite a while and have attempted the skull stripping without much success. I have watched severa…

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## [volume calculation using 2d ct images](https://discourse.slicer.org/t/volume-calculation-using-2d-ct-images/37385)

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**Author:** [@mohammad\_afshari](https://discourse.slicer.org/u/mohammad_afshari)\
**Replies:** 0\
**Last updated:** [July 15, 2024, 7:53pm UTC](https://discourse.slicer.org/t/volume-calculation-using-2d-ct-images/37385 "2024-07-15T19:53:31Z")

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hi folks , we trained a 2d segmentation for traumatic brain hemorrhages using mask-rcnn (detectron2) . it works in 4 class (dural,parenchymal,ventricular,SAH) , now im wondering how can we assess the volume of hemorrhage…

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## [Trying to make 3d model of brain from MRI](https://discourse.slicer.org/t/trying-to-make-3d-model-of-brain-from-mri/6113)

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**Author:** [@tjop92](https://discourse.slicer.org/u/tjop92)\
**Replies:** 12\
**Last updated:** [February 22, 2024, 6:31am UTC](https://discourse.slicer.org/t/trying-to-make-3d-model-of-brain-from-mri/6113 "2024-02-22T06:31:51Z")

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Hello. I am trying to create a 3d model of my brain so that I can 3d print it. I have MRI scans that were done last year. I have no experience with this software or anything like this. I have tried a few tutorials an…

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## [New extension: HDBrainExtraction for AI-based skull stripping](https://discourse.slicer.org/t/new-extension-hdbrainextraction-for-ai-based-skull-stripping/24420)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 15\
**Last updated:** [January 2, 2024, 6:00pm UTC](https://discourse.slicer.org/t/new-extension-hdbrainextraction-for-ai-based-skull-stripping/24420 "2024-01-02T18:00:45Z")

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A new AI-based tool - HDBrainExtracion extension - is added to 3D Slicer for skull stripping (blanking out region outside the brain in MRI images). The model is trained on a large set of images and proven to be more robu…

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## [CTA Brain Extraction / Skull Stripping](https://discourse.slicer.org/t/cta-brain-extraction-skull-stripping/30427)

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**Author:** [@Arpan\_Gyawali](https://discourse.slicer.org/u/Arpan_Gyawali)\
**Replies:** 6\
**Last updated:** [December 29, 2023, 12:44am UTC](https://discourse.slicer.org/t/cta-brain-extraction-skull-stripping/30427 "2023-12-29T00:44:27Z")

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I have a task of extracting Brain or removing skull from a brain CTA scans. To train the model first of all i need to label the mask. I am using 3D slicer segment editor for it. The process I am following is as explained…

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## [Lobes of the brain segmentation from MRI images (T1)](https://discourse.slicer.org/t/lobes-of-the-brain-segmentation-from-mri-images-t1/25337)

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**Author:** [@agatte](https://discourse.slicer.org/u/agatte)\
**Replies:** 3\
**Last updated:** [December 29, 2023, 4:37am UTC](https://discourse.slicer.org/t/lobes-of-the-brain-segmentation-from-mri-images-t1/25337 "2023-12-29T04:37:01Z")

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Hello, I would like to ask you if there is something any tool or module extension to segment lobes of the brain from MRI ?

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## [SlicerBS for brain image segmentation](https://discourse.slicer.org/t/slicerbs-for-brain-image-segmentation/17676)

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**Author:** [@Mehran](https://discourse.slicer.org/u/Mehran)\
**Replies:** 13\
**Last updated:** [August 18, 2023, 3:49am UTC](https://discourse.slicer.org/t/slicerbs-for-brain-image-segmentation/17676 "2023-08-18T03:49:23Z")

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Dear members, I shared a new brain segmentation module using deep learning to extract brain and Tsallis entropy for segmentation. If you work on brain images, please have a look and let me know any feedback. You need t…

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## [Lateral Ventricles of the Brain](https://discourse.slicer.org/t/lateral-ventricles-of-the-brain/29763)

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**Author:** [@elliotw4](https://discourse.slicer.org/u/elliotw4)\
**Replies:** 0\
**Last updated:** [June 1, 2023, 12:08am UTC](https://discourse.slicer.org/t/lateral-ventricles-of-the-brain/29763 "2023-06-01T00:08:56Z")

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I’m currently trying to export STL models of the lateral ventricles of the brain of various sizes: enlarged, average, and slit. Almost all of my smaller or slit ventricle models have some kind of tissue (I believe choroi…

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## [How does HD BET work?](https://discourse.slicer.org/t/how-does-hd-bet-work/29668)

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**Author:** [@MarcoCerciello](https://discourse.slicer.org/u/MarcoCerciello)\
**Replies:** 2\
**Last updated:** [May 26, 2023, 2:44pm UTC](https://discourse.slicer.org/t/how-does-hd-bet-work/29668 "2023-05-26T14:44:36Z")

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I am writing an essay about a brain segmentation I did and I was wondering if some of you could explain me how does the HD Brain Extraction Tool actually work. By reading on the github page, it seems to me that it works …

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## [Heatmap of Brain](https://discourse.slicer.org/t/heatmap-of-brain/25439)

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**Author:** [@lsprs](https://discourse.slicer.org/u/lsprs)\
**Replies:** 0\
**Last updated:** [September 26, 2022, 4:27pm UTC](https://discourse.slicer.org/t/heatmap-of-brain/25439 "2022-09-26T16:27:56Z")

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Hello, I’m interested in finding a way to compare the volume distribution of the brain for patients with various conditions. My plan is to: Obtain CT heads Strip the skull Segment the brain Dynamically visualize the …

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## [Circle of WIllis model from Brain MRI](https://discourse.slicer.org/t/circle-of-willis-model-from-brain-mri/28294)

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**Author:** [@Reasat\_E\_Noor](https://discourse.slicer.org/u/Reasat_E_Noor)\
**Replies:** 0\
**Last updated:** [March 10, 2023, 8:19pm UTC](https://discourse.slicer.org/t/circle-of-willis-model-from-brain-mri/28294 "2023-03-10T20:19:14Z")

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I want to create a model of Circle of Willis from brain MRI Scan. I used vessleness filtering module but didn’t able to view the vessels of brain. Kindly help.

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## [Anatomical brain segmentation](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778)

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**Author:** [@Miglius\_Mikalauskas](https://discourse.slicer.org/u/Miglius_Mikalauskas)\
**Replies:** 5\
**Last updated:** [July 21, 2022, 3:49pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778 "2022-07-21T15:49:27Z")

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Hi. Is there a way to automatically segment human brain in mri by anatomical structures? So that i could automatically see the human brain segmented by either lobes (frontal, temporal etc) or by gyri? The photo is f…

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## [Advice for (Semi-) Automated Segmentation of Neurovasculature](https://discourse.slicer.org/t/advice-for-semi-automated-segmentation-of-neurovasculature/22545)

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**Author:** [@jdh](https://discourse.slicer.org/u/jdh)\
**Replies:** 1\
**Last updated:** [March 16, 2022, 7:39pm UTC](https://discourse.slicer.org/t/advice-for-semi-automated-segmentation-of-neurovasculature/22545 "2022-03-16T19:39:16Z")

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Hello, I have been using Slicer to segment the neurovasculature from MRI datasets of several patients. The focus is on the vessels of the circle of Willis, but I also need to include some of the smaller/darker periphera…

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## [How to segment gray, white and tumor region using NVIDIA clara.](https://discourse.slicer.org/t/how-to-segment-gray-white-and-tumor-region-using-nvidia-clara/21348)

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**Author:** [@Akhil\_Ratan\_Mishra](https://discourse.slicer.org/u/Akhil_Ratan_Mishra)\
**Replies:** 0\
**Last updated:** [January 6, 2022, 5:07pm UTC](https://discourse.slicer.org/t/how-to-segment-gray-white-and-tumor-region-using-nvidia-clara/21348 "2022-01-06T17:07:31Z")

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Operating system: Windows 11 Slicer version: 4.11 Expected behavior: Actual behavior:

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## [How to save brain structural edited masks (segment edited) in nifti for freesurfer use?](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429)

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**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:04am UTC](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429 "2021-07-02T04:04:46Z")

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Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some editing, and I used Slicer Segment Editor for it (opened mask as label \> imported labelmap as segmentation \> …

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## [Brain volume MRI](https://discourse.slicer.org/t/brain-volume-mri/17169)

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**Author:** [@amjadibr](https://discourse.slicer.org/u/amjadibr)\
**Replies:** 1\
**Last updated:** [April 19, 2021, 4:11pm UTC](https://discourse.slicer.org/t/brain-volume-mri/17169 "2021-04-19T16:11:44Z")

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Hi everyone, I am trying to measure the whole brain volume in MRI. I don’t know if the Slicer is the right tool to do it. The result would be numbers representing the volume of the whole brain Thank you in advance

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