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.

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. 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

Reference(s): 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

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

kvlSegmentHippocampalSubfields.sh - program to segment the subfields within the hippocampus

kvlSegmentHippocampalSubfields.sh subjectName side inputDirectory outputDirectory

Running this program requires that the standard volumetric FreeSurfer pipeline has been run first. The output consists of a collection of images in the directory outputDirectory/subjectName/side/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. Visualizing the subregion segmentations on top of the MRI data can be achieved by doing

cd outputDirectory/subjectName/left/segmentationWithoutPartialVolumingLog/ freeview ../nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/data/Atlas3D/FreeSurferColorLUT_edited.txt

for the left side, and analogous for the right side.

Note that, if kvlSegmentHippocampalSubfields.sh was executed by FreeSurfer's recon-all script, recon-all will have copied the results to $SUBJECTS_DIR/subjectName/mri, and you should do

cd $SUBJECTS_DIR/subjectName/mri freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/data/Atlas3D/FreeSurferColorLUT_edited.txt

instead.

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