# \#mri **URL:** https://discourse.slicer.org/tag/mri/12.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [Need CT scans with leksell localizer for validating the transformation to leksell frame co-ordinates in my extension](https://discourse.slicer.org/t/need-ct-scans-with-leksell-localizer-for-validating-the-transformation-to-leksell-frame-co-ordinates-in-my-extension/48116)
**Author:** [@Victor\_Wayne](https://discourse.slicer.org/u/Victor_Wayne)\ **Replies:** 0\ **Last updated:** [September 11, 2026, 5:34am UTC](https://discourse.slicer.org/t/need-ct-scans-with-leksell-localizer-for-validating-the-transformation-to-leksell-frame-co-ordinates-in-my-extension/48116 "2026-09-11T05:34:11Z")
Hi, I am working on an extension in which I have to convert the volumes from RAS co-ordinate system to leksell frame’s XYZ co-ordinate system. I need test data validate my transformation logic. Is there any place where … --- ## [How to segment ligaments on 3D T1w MRI images?](https://discourse.slicer.org/t/how-to-segment-ligaments-on-3d-t1w-mri-images/47705)
**Author:** [@LuuTrinh](https://discourse.slicer.org/u/LuuTrinh)\ **Replies:** 0\ **Last updated:** [July 21, 2026, 2:38pm UTC](https://discourse.slicer.org/t/how-to-segment-ligaments-on-3d-t1w-mri-images/47705 "2026-07-21T14:38:12Z")
Hi everyone, I am working on segmenting ligaments using 3D T1-weighted (T1w) MRI data in 3D Slicer, and I would appreciate some advice on the best workflow/tools for this task. --- ## [Automate bone segmentation from MRI](https://discourse.slicer.org/t/automate-bone-segmentation-from-mri/21530)
**Author:** [@Sezen](https://discourse.slicer.org/u/Sezen)\ **Replies:** 5\ **Last updated:** [July 2, 2026, 9:10am UTC](https://discourse.slicer.org/t/automate-bone-segmentation-from-mri/21530 "2026-07-02T09:10:49Z")
Operating system:Windows 11 I am doing a project on whether it is possible to automate the segmentation of bone from specifically MRI scans however I am new to the software. Can anyone point me in the right direction or… --- ## [Automatic segmentation of the ventricles (brain)](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915)
**Author:** [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\ **Replies:** 7\ **Last updated:** [March 5, 2026, 8:11am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915 "2026-03-05T08:11:07Z")
Hello everyone, I am currently working on hydrocephalus . I wanted to automatically segment the ventricles (brain) and use the volume statistics for research purposes. I tried MONAI Auto3Dseg and nnUnet but I couldn’t f… --- ## [Brain Modelling from MRI images // Help](https://discourse.slicer.org/t/brain-modelling-from-mri-images-help/45841)
**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")
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… --- ## [Volume Rendering not working for MRI](https://discourse.slicer.org/t/volume-rendering-not-working-for-mri/45263)
**Author:** [@Maleia\_Tye](https://discourse.slicer.org/u/Maleia_Tye)\ **Replies:** 3\ **Last updated:** [November 29, 2025, 8:31pm UTC](https://discourse.slicer.org/t/volume-rendering-not-working-for-mri/45263 "2025-11-29T20:31:03Z")
As the title says, I’m not getting a 3D Volume rendering with an MRI. Preface: I’m able to get a 3D Volume view for a CT scan, this seems to only be impacting an MRI. Probably additional helpful information: My project… --- ## [How to detect MRI file being loaded?](https://discourse.slicer.org/t/how-to-detect-mri-file-being-loaded/45079)
**Author:** [@Victor\_Wayne](https://discourse.slicer.org/u/Victor_Wayne)\ **Replies:** 8\ **Last updated:** [November 21, 2025, 9:40am UTC](https://discourse.slicer.org/t/how-to-detect-mri-file-being-loaded/45079 "2025-11-21T09:40:31Z")
Hello, I need to log the header of the MRI file. How can I detect if an MRI file is loaded in slicer? Thanks for your help. --- ## [Need help with analyzing segmentations from 2 different MRIs :( ](https://discourse.slicer.org/t/need-help-with-analyzing-segmentations-from-2-different-mris/44567)
**Author:** [@Mc\_Konni](https://discourse.slicer.org/u/Mc_Konni)\ **Replies:** 1\ **Last updated:** [September 24, 2025, 11:05am UTC](https://discourse.slicer.org/t/need-help-with-analyzing-segmentations-from-2-different-mris/44567 "2025-09-24T11:05:42Z")
Hi Guys, i am completely new to 3D Slicer, i have tried to solve the following issue for a couple of days and im honestly about to give up. Heres my issue: Im conducting research with ULF MR Imaging and have segmentate… --- ## [t1 t2 mr registration](https://discourse.slicer.org/t/t1-t2-mr-registration/43651)
**Author:** [@rafet](https://discourse.slicer.org/u/rafet)\ **Replies:** 1\ **Last updated:** [July 21, 2025, 9:20am UTC](https://discourse.slicer.org/t/t1-t2-mr-registration/43651 "2025-07-21T09:20:18Z")
hello ı am trying to merge two mri of the same patient one is t1 weighted with good sagittal view but limited to the right side of the head and other one is t2 weighted with good axiak view but its contains the whole hea… --- ## [How to convert series (IM files) to one file](https://discourse.slicer.org/t/how-to-convert-series-im-files-to-one-file/41269)
**Author:** [@amirzadeh](https://discourse.slicer.org/u/amirzadeh)\ **Replies:** 1\ **Last updated:** [May 28, 2025, 3:02am UTC](https://discourse.slicer.org/t/how-to-convert-series-im-files-to-one-file/41269 "2025-05-28T03:02:14Z")
Hi. My MRI and CT-Angio images are in a PATH that includes many series folders with IM files that don’t have any extensions. When I add the PATH to 3d slicer it load the images in different series like the images that I’… --- ## [Visualization of lower body muscle segmentation from Dafne](https://discourse.slicer.org/t/visualization-of-lower-body-muscle-segmentation-from-dafne/42452)
**Author:** [@trumanchiu](https://discourse.slicer.org/u/trumanchiu)\ **Replies:** 11\ **Last updated:** [April 30, 2025, 12:45am UTC](https://discourse.slicer.org/t/visualization-of-lower-body-muscle-segmentation-from-dafne/42452 "2025-04-30T00:45:16Z")
Hello everyone, I am new to 3DSlicer and I am working on a lower body MRI study with the goal of segmenting 35 muscles and creating 3D visualizations from the segmentations. Manual muscle segmentations have been complete… --- ## [Shoulder MRI segmentation extension](https://discourse.slicer.org/t/shoulder-mri-segmentation-extension/40152)
**Author:** [@benedettabottelli](https://discourse.slicer.org/u/benedettabottelli)\ **Replies:** 0\ **Last updated:** [November 12, 2024, 5:09pm UTC](https://discourse.slicer.org/t/shoulder-mri-segmentation-extension/40152 "2024-11-12T17:09:52Z")
I need an extension to segment bones, muscles, tendons and ligaments in a shoulder MRI, does it exist? --- ## [Stitching 2 MRI images with deformation.](https://discourse.slicer.org/t/stitching-2-mri-images-with-deformation/39623)
**Author:** [@Haowen\_Wei](https://discourse.slicer.org/u/Haowen_Wei)\ **Replies:** 0\ **Last updated:** [October 9, 2024, 11:23pm UTC](https://discourse.slicer.org/t/stitching-2-mri-images-with-deformation/39623 "2024-10-09T23:23:55Z")
Hello 3D Slicer Community, I am working with two MRI images of a leg—one capturing the upper section and the other covering the lower section. There is an overlap between these two images, but unfortunately, the regions… --- ## [Fusion MRI and PET](https://discourse.slicer.org/t/fusion-mri-and-pet/38388)
**Author:** [@Pavel\_Pakhomov](https://discourse.slicer.org/u/Pavel_Pakhomov)\ **Replies:** 0\ **Last updated:** [September 15, 2024, 5:25am UTC](https://discourse.slicer.org/t/fusion-mri-and-pet/38388 "2024-09-15T05:25:20Z")
Hello? i’m new user ) I have problems )) I have mri dicom (pelvis) and PET/CT FDG-psma scans I need to fuse T2 iso with PET images, and that save this to dicom for US-navigation; i used landmark registration, and i saw n… --- ## [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)
**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")
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… --- ## [Slope and intercept for pixel intensity MRI](https://discourse.slicer.org/t/slope-and-intercept-for-pixel-intensity-mri/37400)
**Author:** [@IrisM](https://discourse.slicer.org/u/IrisM)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 3:42pm UTC](https://discourse.slicer.org/t/slope-and-intercept-for-pixel-intensity-mri/37400 "2024-07-17T15:42:13Z")
I want to use 3D slicer to extract first order features with the radiomics module from RTstructs of MRI images. However, I want all the pixel intensities from my MR image to be adapted first by a certain slope and interc… --- ## [Tools for Making Sagittal, Coronal, and Transverse Cuts in MRI Models](https://discourse.slicer.org/t/tools-for-making-sagittal-coronal-and-transverse-cuts-in-mri-models/37163)
**Author:** [@Maria\_Ardila](https://discourse.slicer.org/u/Maria_Ardila)\ **Replies:** 0\ **Last updated:** [July 3, 2024, 3:48am UTC](https://discourse.slicer.org/t/tools-for-making-sagittal-coronal-and-transverse-cuts-in-mri-models/37163 "2024-07-03T03:48:56Z")
Hello, I have this model that I obtained from an MRI scan. Is there any tool or method to make sagittal, coronal, and transverse cuts to this 3D object? It would be very helpful. --- ## [Problem loading MRI scan. Only one view, axial, is clear, the other two are blurry](https://discourse.slicer.org/t/problem-loading-mri-scan-only-one-view-axial-is-clear-the-other-two-are-blurry/1799)
**Author:** [@olivya\_caballero](https://discourse.slicer.org/u/olivya_caballero)\ **Replies:** 7\ **Last updated:** [June 19, 2024, 11:39pm UTC](https://discourse.slicer.org/t/problem-loading-mri-scan-only-one-view-axial-is-clear-the-other-two-are-blurry/1799 "2024-06-19T23:39:28Z")
Operating system: Windows 10 Slicer version: 4.8.0 Expected behavior: All three views are clear Actual behavior: Only axial is clear and the other views are a bit titled and blurry. Unable to get a good 3d model out o… --- ## [Bone Segmentation for MRI scans](https://discourse.slicer.org/t/bone-segmentation-for-mri-scans/36381)
**Author:** [@BDA](https://discourse.slicer.org/u/BDA)\ **Replies:** 4\ **Last updated:** [May 29, 2024, 11:56am UTC](https://discourse.slicer.org/t/bone-segmentation-for-mri-scans/36381 "2024-05-29T11:56:04Z")
Operating system: windows Slicer version: 5.6.2 Expected behavior: creating 3D bone models from MR images Actual behavior: I want to create 3D bone models from MRI scans…I have MR images of the shoulder and knee regi… --- ## [Trying to make 3d model of brain from MRI](https://discourse.slicer.org/t/trying-to-make-3d-model-of-brain-from-mri/6113)
**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")
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… --- ## [How to analyze DCE-MRI data](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622)
**Author:** [@kirezgik](https://discourse.slicer.org/u/kirezgik)\ **Replies:** 51\ **Last updated:** [January 11, 2024, 11:41am UTC](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622 "2024-01-11T11:41:11Z")
Operating system: Microsoft Windows 7 Enterprise Slicer version: Slicer 4.7.0 nightly build Expected behavior: Quantitative analysis of DCE MRI and measuring parameters like K trans and fractional value Actual behavior:… --- ## [Lobes of the brain segmentation from MRI images (T1)](https://discourse.slicer.org/t/lobes-of-the-brain-segmentation-from-mri-images-t1/25337)
**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")
Hello, I would like to ask you if there is something any tool or module extension to segment lobes of the brain from MRI ? --- ## [Novice Guidance for Using MONAI Label to Create an Automatic Segmentation App](https://discourse.slicer.org/t/novice-guidance-for-using-monai-label-to-create-an-automatic-segmentation-app/27504)
**Author:** [@JacobD](https://discourse.slicer.org/u/JacobD)\ **Replies:** 20\ **Last updated:** [November 21, 2023, 5:49am UTC](https://discourse.slicer.org/t/novice-guidance-for-using-monai-label-to-create-an-automatic-segmentation-app/27504 "2023-11-21T05:49:32Z")
I attended the recent MONAI Label Workshop, and with a background of sports medicine/orthopaedics research, I am new to this concept and do not have a strong background in computer programming. I am familiar with 3D Slic… --- ## [PET-MRI corregistration](https://discourse.slicer.org/t/pet-mri-corregistration/32346)
**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\ **Replies:** 0\ **Last updated:** [October 20, 2023, 3:03pm UTC](https://discourse.slicer.org/t/pet-mri-corregistration/32346 "2023-10-20T15:03:11Z")
Hi: I have some whole body PET-CT images, and liver MRI (patients with liver cancer). How can I do a PET-MRI corregistration? Sincerely, Gonzalo Rojas Costa --- ## [Carotid Artery Segmentation in tw weighted MRI's](https://discourse.slicer.org/t/carotid-artery-segmentation-in-tw-weighted-mris/31866)
**Author:** [@Redalligator291](https://discourse.slicer.org/u/Redalligator291)\ **Replies:** 0\ **Last updated:** [September 24, 2023, 2:53am UTC](https://discourse.slicer.org/t/carotid-artery-segmentation-in-tw-weighted-mris/31866 "2023-09-24T02:53:55Z")
Hi guys, I am very new to 3D slicer and medical images in general. I am trying to segment the carotid arteries in a t2-weighted image. However, I am having trouble doing that. I think fundamentally, I am having trouble k… --- ## [Bone segmentation through MRI scan dicom images](https://discourse.slicer.org/t/bone-segmentation-through-mri-scan-dicom-images/31786)
**Author:** [@Bibi\_Ayisha](https://discourse.slicer.org/u/Bibi_Ayisha)\ **Replies:** 2\ **Last updated:** [September 21, 2023, 1:17pm UTC](https://discourse.slicer.org/t/bone-segmentation-through-mri-scan-dicom-images/31786 "2023-09-21T13:17:13Z")
I was provided a MRI scan of a patient. I have seen different series in the data and the data does not load completely. If I load all the files together it is not showing images properly. Is the issue related to dicom im… --- ## [MultiVolume Explorer and Segment Editor Error](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732)
**Author:** [@aginn](https://discourse.slicer.org/u/aginn)\ **Replies:** 22\ **Last updated:** [August 31, 2023, 2:04am UTC](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732 "2023-08-31T02:04:23Z")
Hi all - I am trying to load a cine-MRI (link to data is below). I was able to import it through the DICOM import, but the results look off. Furthermore, when I go to “volume rendering,” there is no volume generated, bu… --- ## [Inquiry Regarding Measurement of Functional Tumor Volume in Breast using 3D Slicer](https://discourse.slicer.org/t/inquiry-regarding-measurement-of-functional-tumor-volume-in-breast-using-3d-slicer/31188)
**Author:** [@thomas\_su](https://discourse.slicer.org/u/thomas_su)\ **Replies:** 3\ **Last updated:** [August 18, 2023, 12:36pm UTC](https://discourse.slicer.org/t/inquiry-regarding-measurement-of-functional-tumor-volume-in-breast-using-3d-slicer/31188 "2023-08-18T12:36:53Z")
Dear 3D Slicer Community, Currently, I am delving into the realm of measuring Functional Tumor Volume (FTV) in breast tumors, along with parameters like Percentage of Enhancement (PE) and Signal Enhancement Ratio (SER).… --- ## [Automatically split segmentation islands connected by a narrow path](https://discourse.slicer.org/t/automatically-split-segmentation-islands-connected-by-a-narrow-path/30938)
**Author:** [@nasibov\_98](https://discourse.slicer.org/u/nasibov_98)\ **Replies:** 4\ **Last updated:** [August 3, 2023, 1:20pm UTC](https://discourse.slicer.org/t/automatically-split-segmentation-islands-connected-by-a-narrow-path/30938 "2023-08-03T13:20:49Z")
Hi there, I have a simple question. I am using the segment islands tool to separate tumours that are not touching each other into unique segments. How do I separate tumours that are touching each other i.e. have narro… --- ## [Signal loss through slices in sample. Need Cause and Post-Processing suggestions](https://discourse.slicer.org/t/signal-loss-through-slices-in-sample-need-cause-and-post-processing-suggestions/30611)
**Author:** [@nasibov\_98](https://discourse.slicer.org/u/nasibov_98)\ **Replies:** 2\ **Last updated:** [July 17, 2023, 3:43pm UTC](https://discourse.slicer.org/t/signal-loss-through-slices-in-sample-need-cause-and-post-processing-suggestions/30611 "2023-07-17T15:43:41Z")
Hi, I am working on a project to segment tumours and livers automatically in FLASH axial images of mouse livers. There is progressive signal loss as I approach the bottom-most slices in a 45 slice image. I have attached… [Next page](https://discourse.slicer.org/tag/mri/12.md?match_all_tags=true&page=1&tags%5B%5D=mri)