Help with Lobe Segmentation and 3D Visualization in FreeSurfer

[Samar_Boulehmi]

Hello everyone,

I’m working on segmenting and visualizing the cerebral lobes from T1-weighted MRI scans using FreeSurfer. My objective is to:

1. Segment the cerebral lobes from T1 MRI.
2. Assign each lobe a different label and visualize them in 3D.
3. Register the segmented lobes onto the original T1 scan for clear visualization.
   I followed these steps in FreeSurfer:
   Ran the full FreeSurfer pipeline:
   recon-all -s my_subject -i T1.mgz -all
   Converted the parcellation to individual labels:
   mri_annotation2label --subject my_subject --hemi lh --annotation aparc.DKTatlas --outdir labels/
   **Merged the labels into lobe-specific segmentations:
   mri_mergelabels labels/lh.*.label -o lh_lobes.label
   Converted the label files into volumetric images:
   mri_label2vol --label lh_lobes.label --temp T1.mgz --o sujet1t1.nii --identity

The Problem:

• The output does not display as expected. Instead of solid, colored lobes, I see only contours outlining the regions
  

  

• Applying --apply_lut does not seem to fix the issue.

• I tried mri_binarize to ensure the labels were filled, but it didn’t change the visualization much.

Does anyone have experience with this type of segmentation? How can I ensure that each lobe is properly labeled, filled, and visualized in 3D correctly? Any help would be greatly appreciated!

Thank you in advance