Brain MRI Gray Matter Segmentation

klippert · June 5, 2022, 10:33pm

Dear Community,

I’m just a 3d printing nerd looking to print my brain from MRI/DCOM files. I’ve been able to extract my brain using HD-BET and Swiss Skull Stripper. Now I’m trying to just isolate the gray matter/cerebral cortex/folds, etc. However, when I use thresholding in segment editor on the extracted brain segment, I can’t seem to get the structure definition on the sides/rear (too smooth) of my brain as shown in the pics.

If anyone has a step by step tutorial I would greatly appreciated it. I’m just trying to develop a recipe to 3d print brains for myself and family.

I found a brain logistic segmentation extension in the attached pic. This appears to isolate gray/white matter in 3d slicer, but not sure how to install it? I don’t see it in the list of extensions inside 3d slicer, but I guess there is a way to download the python files, but not that familiar with how to install manually and what sub directory to add it to?

Any help would be appreciated.

Thanks,
Kurt

pieper · June 5, 2022, 10:48pm

You can maybe try FreeSurfer directly, or if it’s not working you can use SynthSeg and run the results through FreeSurfer. You can work with the results in Slicer.

klippert · June 6, 2022, 3:05am

I think this 3d slicer extension could isolate the gray matter and cortical structures. However, I don’t see this extension in the extension module list inside 3d slicer v5.0.2 (Mac).

Brain Tissues Extension:

https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BrainTissuesExtension

Thanks,
Kurt

mau_igna_06 · June 6, 2022, 8:19am

why don’t you try this one?

github.com

Slicer/ExtensionsIndex/blob/master/HDBrainExtraction.s4ext

#
# First token of each non-comment line is the keyword and the rest of the line
# (including spaces) is the value.
# - the value can be blank
#

# This is source code manager
scm git
scmurl https://github.com/lassoan/SlicerHDBrainExtraction.git
scmrevision main

# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
depends PyTorch

# Inner build directory (default is ".")
build_subdirectory .

# homepage

This file has been truncated. show original

tyou can download it from the extesnsions manager

Mauro

klippert · June 6, 2022, 1:43pm

The link you provided appears to be the HDBrainExtraction (HD-BET) Extension, that’s what I used to generate the skull stripped brain volume (in blue) in my pictures. This is a great extension and easy to use, but I think it still retains portions of the meninges layers. I’ve used the extracted/segmented volume from HD-BET and applied thresholding in segment editor to get the results in the pics attached, but I can’t seems to isolate just the gray matter in the rear/sides of the extracted brain. So I’ve found a couple gray matter segmentation extensions, but they are not available in the extensions manager list in 3d slicer.

Are there any instructions on how to install an extension like “Brain Tissues” extension with code on Github into 3d Slicer manually? I’m assuming I would have to download the files from Github for the specific extension and copy to a folder on my Mac that 3d slicer would install? Can I use “Extension Wizard” to load an extension manually? I’m a coding novice, so have no clue.

Thanks,
Kurt

slicer365 · June 6, 2022, 11:48pm

I have installed this module, but it does’t work. The last version was updated before 5 years.

klippert · June 7, 2022, 1:29am

Agreed, I was able to get it to load, but when it ran on my volume it did not isolate the gray matter. Any guidance on doing this in segment editor with thresholding or other method would be appreciated.

mau_igna_06 · June 7, 2022, 9:17am

Please see if this one it’s useful

github.com

Slicer/ExtensionsIndex/blob/2a2ba15f045e5bfcb5e86c455dea6d9e1d03c265/ARCHIVE/ROBEXBrainExtraction.s4ext

#
# First token of each non-comment line is the keyword and the rest of the line
# (including spaces) is the value.
# - the value can be blank
#

# This is source code manager (i.e. svn)
scm git
scmurl https://github.com/CSIM-Toolkits/ROBEXBrainExtraction.git
scmrevision ac25d08

# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
depends NA

# Inner build directory (default is ".")
build_subdirectory .

# homepage

This file has been truncated. show original

klippert · June 7, 2022, 2:02pm

Mauro, sorry for being so high maintenance, will ROBEX work on a Mac? I’ve tried loading it and get this error, I just copied the extension file into a folder robex3 and used the extension wizard to “select extension” and directed it to the robex3 folder. Do I need to download other files?

mau_igna_06 · June 7, 2022, 4:42pm

@jcfr @pieper @lassoan do you think you could check why this twño brain extensions are apparently not working?

Thank you

pieper · June 7, 2022, 4:51pm

That extension is several years old and apparently is not maintained. Contacting the original authors could help.

I still suggest the methods I suggested earlier.

jarrett-rushmore · June 8, 2022, 9:23pm

Hi Kurt,
I agree with Steve and would suggest FreeSurfer. Segmentation may not do super well at isolating a number of sulci and may make the brain look lisencephalic in parts, but the FreeSurfer produces surfaces that typically do a nice job and help to create useful segmentations. You can then import the surfaces and related segmentations using the FreeSurfer Importer Extension for Slicer, which is really really nice. Good luck!
Jarrett

Mehran · June 9, 2022, 12:06pm

Hi, you can try our latest module to extract brain and segment GM/WM/CSF way better than freesurfer. You will find link to download and how to install as follow

klippert · June 11, 2022, 4:33am

Mehran,

Thanks for the link, I loaded TSALLIS extension and having some issues extracting the entire brain and then segmenting it to just get the gray matter. I had to set the extraction parameter close to 0 to cover all the brain and still has holes. Then I’m not sure what segmentation values to use to just get the gray matter. I then modified the segment output in segment editor and used the threshold function to create a 3d version, but it still has some areas in the rear/sides that are smooth. I like your extension, but think either my MRI/DCOM files are not high enough resolution or I just have incorrect settings in your extension?

Thanks,
Kurt

klippert · June 11, 2022, 5:15am

Pics of 3d brain after using threshold on LabelMapVolume_1 output from Tsallis segmentation.

Tsallis Values:
Extraction Parameter = 0.1
q parameter = -0.64
alpha = 0.5
beta = 0.5
gama = 0
iteration = 1

Mehran · June 12, 2022, 1:50pm

Hi Kurt,
It might be because of artifact or resolution that all brain is not extracted. You may use N4 Bias correction, noise remove, … to improve the results. If you want, you can send your image to have a look.
Best,

dr_usman_sani · November 18, 2023, 1:33pm

hi my question is not relevant to your querry but i am begginer how this happend that your T2 axial image is not distorted in other planes ( sagittal and coronal)i cannot get rid of leggo shaped/staircase artefact.

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Brain MRI Gray Matter Segmentation

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