How can I segment T1W MRI and produce its image mask?

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I currently have a task at hand which has been challenging for me. I wish to produce a mask image (to be in .nii format) from a T1-weighted image (which is in .nii format and containing a glioma region). Before producing this image, I wish to segment the image into:

  1. White matter
  2. Grey matter
  3. CSF
  4. Tumour (if possible, with peritumoral edema region)

I would be very glad to get your recommendations and suggestions on the best way this task could be done with 3D slicer. I would not mind articles and lectures notes.

By the way, is it possible to also extract out only CSF regions and save as xxx.nii?

Many thanks in advance.

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I don’t think there’s an off-the-shelf automated way of doing all of that currently, but if anybody knows of one I hope they will post here.

There are several pieces available and with a bit of manual work you can put together a nice segmentation.

For example the models trained on BraTS are getting very good at tumor and edema. E.g. this one has been made available for Slicer. Other tools like SynthSeg are very good at non-tumor brain segmentation (including CSF). You can manually combine the results of these and fix errors with the Segment Editor and extract CSF masks and other structures.

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I don’t know what Slicer offers for this task directly, but here is an approach I have taken before using antspy prior-based segmentation. Below is a sketch of the code to give the idea; I haven’t tested this code directly.

import ants

# This method of segmentation uses registration to
# an atlas that comes with a known segmentation
# I have used SRI24 in the past: https://www.nitrc.org/projects/sri24/

# Load atlas
atlas_img = ants.image_read(path_to_T1_atlas)
atlas_csf_img = ants.image_read(path_to_csf_segment_of_atlas)
atlas_gm_img = ants.image_read(path_to_gm_segment_of_atlas)
atlas_wm_img = ants.image_read(path_to_wm_segment_of_atlas)

# Load input image
img = ants.image_read(path_to_input_image)

# Run N4 bias correction
img_n4 = ants.n4_bias_field_correction(img)

# Register to atlas
img_reg = ants.registration(atlas_img, img_n4)

# create mask to restrict the segmentation inside this region
priors = [atlas_csf_img, atlas_gm_img, atlas_wm_img]
mask = priors[0].copy()
mask_view = mask.view()
for i in range(1, len(priors)):
    mask_view[priors[i].numpy() > 0] = 1
mask_view[mask_view > 0] = 1

# Do prior-based segmentation
seg = ants.prior_based_segmentation(img_reg, priors, mask)

# Take csf label
seg_img_view = seg['segmentation'].view()
csf_img = seg['segmentation'].copy()
csf_img_view = feature_img.view()
csf_img_view.fill(0)
csf_img_view[seg_img_view == 1] = 1  # 1 is the CSF label

# Write to nifti file
ants.image_write(csf_img, "csf_mask.nii.gz")
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