# Whole brain automate segmentation

**URL:** <https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225>\
**Category:** Support\
**Created:** [December 27, 2021, 2:01am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225 "2021-12-27T02:01:42Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![mahinaz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mahinaz/32/13759_2.png) [@mahinaz](https://discourse.slicer.org/u/mahinaz)\
**Post date:** [December 27, 2021, 2:01am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/1 "2021-12-27T02:01:42Z")

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Hello . i am using two mri PD images of one patient in 2 consecutive year of his disease.  
i done below steps :

1. i registered two images by General Registration Module ( fixed image was the image of patient in 2012 and moving image was image of patient in 2014)
2. i applied Median Filter and i used from this Module for smoothing my images.
3. i removed skull of brain by Swiss Skull Remove Module.  
and now i want to segment whole brain automaticlly specially GM and WM and Basal Ganglia. how should i do this?  
more explain: i used from segment editor module for segmentation but it’s results weren’t satisfactory.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 29, 2021, 12:06am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/2 "2021-12-29T00:06:03Z")

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I suggest [SynthSeg](https://github.com/BBillot/SynthSeg). I’ve had good luck with it on a wide variety of scans. There’s no Slicer extension for it (yet?) but you can run it from the command line and use the results in Slicer.

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**Author:** ![mahinaz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mahinaz/32/13759_2.png) [@mahinaz](https://discourse.slicer.org/u/mahinaz)\
**Post date:** [December 29, 2021, 12:17am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/3 "2021-12-29T00:17:30Z")

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Thanks for your guidness. And how about FSL software? not freesurfer

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 29, 2021, 12:44am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/4 "2021-12-29T00:44:40Z")

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FSL has good tools too, but I haven’t used them myself.

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**Author:** ![mahinaz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mahinaz/32/13759_2.png) [@mahinaz](https://discourse.slicer.org/u/mahinaz)\
**Post date:** [December 29, 2021, 12:59am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/5 "2021-12-29T00:59:05Z")

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And i think i can import my data from FreeSurfer by FreeSurfer Importer module.right?

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 29, 2021, 4:25am UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/6 "2021-12-29T04:25:25Z")

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Yes, the [SlicerFreeSurfer](https://github.com/PerkLab/SlicerFreeSurfer) extension should work well. But traditional FreeSurfer requires high resolution T1 data, where SynthSeg (which comes from many of the same developers) is robust for different resolutions and contrasts.

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**Author:** ![Greydon\_Gilmore](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/greydon_gilmore/32/6863_2.png) [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Post date:** [January 1, 2022, 9:14pm UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/7 "2022-01-01T21:14:17Z")

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I’ve had some success with Atropos from ANTS ([An open source multivariate framework for n-tissue segmentation with evaluation on public data - PubMed](https://pubmed.ncbi.nlm.nih.gov/21373993/)).

The segmentation tool from FSL is called FAST ([FAST - FslWiki](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST)).

If you choose FreeSurfer I suggest looking into FastSurfer ([GitHub - Deep-MI/FastSurfer: PyTorch implementation of FastSurferCNN](https://github.com/Deep-MI/FastSurfer)). segmentation finishes in half the time.

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**Author:** ![mahinaz](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mahinaz/32/13759_2.png) [@mahinaz](https://discourse.slicer.org/u/mahinaz)\
**Post date:** [January 22, 2022, 7:43pm UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/8 "2022-01-22T19:43:12Z")

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thanks. i segmented my images in 6 chapter by fsl. now i want to crop a region very accurately with high accuracy. with which tool in 3dslicer can i do this?  
should i do this automaticlly?

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 24, 2022, 9:11pm UTC](https://discourse.slicer.org/t/whole-brain-automate-segmentation/21225/9 "2022-01-24T21:11:21Z")

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You can use “Crop volume” module crop with an axis-aligned rectangular prism shaped region. You can clip the image using freehand shapes using Segment Editor module. Both performs pixel-perfect cropping: nothing is changed in the image except the cropped regions are removed or blanked out.