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| 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. |
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 |
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| ./recon-all -s bert -all -hippo-subfields | recon-all -s bert -all -hippo-subfields |
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| ./recon-all -s bert -hippo-subfields | recon-all -s bert -hippo-subfields |
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| 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 |
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 |
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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 |
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kvlSegmentHippocampalSubfields.sh - program to segment the subfields within the hippocampus kvlSegmentHippocampalSubfields.sh subjectName side inputDirectory outputDirectory 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. 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. 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> kvlQuantifyHippocampalSubfieldSegmentations.sh |
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>