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…

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 .

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 Than…

why don’t you try this one? 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:…

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/se…

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

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.

Please see if this one it’s useful 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 # …

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? [IMG_…

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

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.

Brain MRI Gray Matter Segmentation

Support

Mehran (Mehran) June 9, 2022, 12:06pm 13

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

Topic		Replies	Views
Segmenting out a brain in an MRI Support segmentation	6	6402	May 16, 2024
Brain Tissues Extension not found/Separating Brain Tissues Support segmentation , extensions-manager	1	222	February 17, 2026
Assistance with Brain MR segmentation? Support	1	43	March 2, 2026
Automated brain segmentation into White Matter Volume, GMV, and CSF Vol? Support segmentation , extensions-manager	6	1913	August 27, 2021
Brain Segmentation in MR Support segmentation , brain	5	506	July 19, 2024

Brain MRI Gray Matter Segmentation

Related topics