Segmentation of hippocampal subfields

Author: Koen Van Leemput

See also: GEMS

Automated segmentation of the subfields of the hippocampus, using models built from manual segmentations of the right hippocampus in 0.38x0.38x0.8 mm^3 in vivo MRI scans in 10 subjects. For the left hippocampus, the model for the right side is simply mirrored. The exact algorithm is described in the paper:

To generate the hippocampal subfield segmentations as part of the normal FreeSurfer processing stream, simply add the "-hippo-subfields" flag to the recon-all script:

 recon-all -s bert -all -hippo-subfields

It is also possible to only run the hippocampal subfield segmentation for a subject that has already undergone the standard volumetric FreeSurfer pipeline (in particular, the program needs the FreeSurfer-generated files "aseg.mgz", "nu.mgz" and "talairach.xfm"):

 recon-all -s bert -hippo-subfields

The output consists of a collection of images $SUBJECTS_DIR/bert/mri/posterior_* that indicate each voxel's posterior probability of belonging to different subregions. The estimated volumes of these subregions can be obtained using the "kvlQuantifyHippocampalSubfieldSegmentations.sh" script. Doing

 cd $SUBJECTS_DIR
 kvlQuantifyHippocampalSubfieldSegmentations.sh

will create the text files "nonPartialVolumeStatsLeft.txt" and "nonPartialVolumeStatsRight.txt" in the directory $SUBJECTS_DIR, containing tables that summarize the volumes of the hippocampal subfield segmentations of the left and right side, respectively, in all of the subjects in $SUBJECTS_DIR. The reported volumes are given in number of voxels, where each voxel is of the size "0.5x0.5x0.5mm^3". It is expected that the "-hippo-subfields" flag has been used for each subject in $SUBJECTS_DIR.

Visualizing the subregion segmentations on top of the MRI data can be achieved by doing

 cd $SUBJECTS_DIR/bert/mri
 freeview nu.mgz -p-labels posterior_left_* \
  posterior_right_* \
  posterior_Left-Hippocampus.mgz \
  posterior_Right-Hippocampus.mgz \
  -p-prefix posterior_ \
  -p-lut $FREESURFER_HOME/data/GEMS/FreeSurferColorLUT_edited.txt

Report bugs to <freesurfer@nmr.mgh.harvard.edu>