Segmentation of hippocampal subfields

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:

• Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI. K. Van Leemput, A. Bakkour, T. Benner, G. Wiggins, L.L. Wald, J. Augustinack, B.C. Dickerson, P. Golland, B. Fischl. Hippocampus, vol. 19, no. 6, pp. 549-557, June 2009

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/Atlas3D/FreeSurferColorLUT_edited.txt

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