# \#automation **URL:** https://discourse.slicer.org/tag/automation/250.md [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) --- ## [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… --- ## [Automatize model generation from segmentation](https://discourse.slicer.org/t/automatize-model-generation-from-segmentation/35355)
**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\ **Replies:** 5\ **Last updated:** [April 29, 2024, 4:20pm UTC](https://discourse.slicer.org/t/automatize-model-generation-from-segmentation/35355 "2024-04-29T16:20:30Z")
Hi, I would like to automatically generate 3D-models from segmented 3D-data. The segmented data is stored as \*.nrrd, and the segmentation was performed with an external program. The idea is to store the segmented dat… --- ## [Run Python code in each subfolder automatically](https://discourse.slicer.org/t/run-python-code-in-each-subfolder-automatically/33924)
**Author:** [@paleomariomm](https://discourse.slicer.org/u/paleomariomm)\ **Replies:** 2\ **Last updated:** [January 23, 2024, 3:59pm UTC](https://discourse.slicer.org/t/run-python-code-in-each-subfolder-automatically/33924 "2024-01-23T15:59:04Z")
I have this file structure: Main Folder: W001-W100. Subfolder: W001 Around 500 DICOM files (I am working with CT data). Subfolder: W002 Around 500 DICOM files (I am working with CT data). Subfolder: ... … --- ## [Automating the process of getting surface models from 1000 CTs](https://discourse.slicer.org/t/automating-the-process-of-getting-surface-models-from-1000-cts/33831)
**Author:** [@paleomariomm](https://discourse.slicer.org/u/paleomariomm)\ **Replies:** 4\ **Last updated:** [January 18, 2024, 12:34pm UTC](https://discourse.slicer.org/t/automating-the-process-of-getting-surface-models-from-1000-cts/33831 "2024-01-18T12:34:21Z")
Dear community. We have 1000 baboon scans in DICOM files. In our research, we thought and tested a pipeline to work with each of them. First, we need to crop the volume as all of them show a platform placed centimete… --- ## [Segmentation size measurements (craniocaudal length and max diameter) to table](https://discourse.slicer.org/t/segmentation-size-measurements-craniocaudal-length-and-max-diameter-to-table/20825)
**Author:** [@rrp](https://discourse.slicer.org/u/rrp)\ **Replies:** 11\ **Last updated:** [November 29, 2023, 12:55pm UTC](https://discourse.slicer.org/t/segmentation-size-measurements-craniocaudal-length-and-max-diameter-to-table/20825 "2023-11-29T12:55:45Z")
Operating system: Windows 11 Home Slicer version: 4.11.20200930 Hi, It is my first time writing in this forum. I would like to measure the craniocaudal length and max diameter (in axial plane) of a segmentation. Actu… --- ## [Select point (user input) on 3D surface for 2000 surfaces automatically opening after user selects a point](https://discourse.slicer.org/t/select-point-user-input-on-3d-surface-for-2000-surfaces-automatically-opening-after-user-selects-a-point/29164)
**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\ **Replies:** 3\ **Last updated:** [May 9, 2023, 8:39am UTC](https://discourse.slicer.org/t/select-point-user-input-on-3d-surface-for-2000-surfaces-automatically-opening-after-user-selects-a-point/29164 "2023-05-09T08:39:38Z")
Hi Andras, Would it be possible to select the point (x,y,z) location in a ply file, for all the ply files opening up one by one and closing once the point is selected. The point needed to be selected by the user on the… --- ## [Processing of a large number of MRIs](https://discourse.slicer.org/t/processing-of-a-large-number-of-mris/26006)
**Author:** [@tsinesh](https://discourse.slicer.org/u/tsinesh)\ **Replies:** 0\ **Last updated:** [November 1, 2022, 5:09pm UTC](https://discourse.slicer.org/t/processing-of-a-large-number-of-mris/26006 "2022-11-01T17:09:35Z")
How can I perform an analysis on a large data set with e.g. 800 MRIs? I imagine to process all images uniformly as far as possible automatically in a loop: e.g. N4 homogenization algorithm for MRI Bias Field Correction … --- ## [Registration method for automatically segmented 2D US slices](https://discourse.slicer.org/t/registration-method-for-automatically-segmented-2d-us-slices/22717)
**Author:** [@Marijn\_H](https://discourse.slicer.org/u/Marijn_H)\ **Replies:** 0\ **Last updated:** [March 28, 2022, 10:42am UTC](https://discourse.slicer.org/t/registration-method-for-automatically-segmented-2d-us-slices/22717 "2022-03-28T10:42:29Z")
I am trying to automatically register tracked US images to a CT scan (with 3D model). I already developed a way to automatically segment bone from US images in real-time. The segmented binary image can be loaded in slice… --- ## [Multi-trial landmarking using SlicerMorph](https://discourse.slicer.org/t/multi-trial-landmarking-using-slicermorph/21668)
**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")
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… --- ## [Automation of creating voxel histograms of segmentation data](https://discourse.slicer.org/t/automation-of-creating-voxel-histograms-of-segmentation-data/18736)
**Author:** [@Griffin](https://discourse.slicer.org/u/Griffin)\ **Replies:** 3\ **Last updated:** [July 14, 2021, 7:59pm UTC](https://discourse.slicer.org/t/automation-of-creating-voxel-histograms-of-segmentation-data/18736 "2021-07-14T19:59:41Z")
I am fairly new to 3d slicer but I am trying to figure out how and I automate or speed up the process of getting a histogram of voxel data from a segmented section. I have been able to do this for one segment at a time t… --- ## [Segmenting on an oblique plane 2D image](https://discourse.slicer.org/t/segmenting-on-an-oblique-plane-2d-image/14215)
**Author:** [@mk.kassai](https://discourse.slicer.org/u/mk.kassai)\ **Replies:** 5\ **Last updated:** [January 31, 2021, 6:03pm UTC](https://discourse.slicer.org/t/segmenting-on-an-oblique-plane-2d-image/14215 "2021-01-31T18:03:00Z")
I would like to do segmentation of a single slice of MRI, that has been acquired in an oblique angle. If I load it into 3D slicer, I only get some lines in different directions, since it shows the X Y and Z plane cross … --- ## [Automate import-segmentation-export process for bronchial tree](https://discourse.slicer.org/t/automate-import-segmentation-export-process-for-bronchial-tree/10617)
**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\ **Replies:** 4\ **Last updated:** [March 12, 2020, 2:21pm UTC](https://discourse.slicer.org/t/automate-import-segmentation-export-process-for-bronchial-tree/10617 "2020-03-12T14:21:53Z")
Hello, I have used 3DSlicer for a few years now, but have not attempted to automate any processes. My group is interested in segmenting air-filled structures and cavities, which ends-up becoming a very simple and consi…