##This repository contains scripts for multi-atlas based hypothalamus segmentation. Input is an anatomical T1-weighted image (ideally 1 mm isotropic, acquired with the ADNI-protocol). Output will be binary left and right hypothalamus segmentations.

for details please see: Thomas, K., Beyer, F., Witte, A.V.: "Altered hypothalamic microstructure in human obesity" https://www.biorxiv.org/content/10.1101/593004v1

Steps in the algorithm: 1.non-linear registration of the T1-weighted image to an intermediate template 2.non-linear registration of atlas images to target image in template space 3.propagation of hypothalamic segmentations from the atlas images (N=44 in total) to the target space 4.merging hypothalamic segmentations and label fusion

To perform the steps described in Algorithm: Step 1, 2, 3: labelpropagation/labelpropagation.py

• TO DO: adapt paths to atlas files/target files/list of atlas and target SICs/ working directory/ output directory
• helper functions (don't modify anything here) are warp_transform_with_datagrabber.py quick_registration.py ants_registration_wf_parallel.py

Step 4.: /fusion/merge_results.sh

• bash-script to merge and binarize hypothalamic segmentations that were propagated from atlas images to target space
• TO DO: adapt paths to results from labelpropagation.

/fusion/runstaple.py

• TO DO: adapt paths to results from merge_results.
• merges binarized hypothalamic segmentations from all atlas images with the STEPS algorithm implemented in NiftySeg (https://github.com/KCL-BMEIS/NiftySeg/tree/master/seg-apps), wrapped in nipype (https://nipype.readthedocs.io/en/latest/interfaces/generated/interfaces.niftyseg/label_fusion.html#labelfusion)

For template and atlas images from the LIFE-Adult study, please visit: https://edmond.mpdl.mpg.de/imeji/collection/QEBGeGdvAXHCaS8m

#Atlas images N44_atlas_images.txt: SIC (subject identification codes) of 44 atlas subjects. atlasimages.tar.gz: contains folders of atlas subjects with the following files:

XXX_MPRAGE_t1_reorient_16bit_acpc_noz0_skullstrippedRepaired.nii.gz: original T1 image XXX_hyp_re_swapped_RAS.nii.gz: semi-automatically, manually segmented right hypothalamus XXX_hyp_li_swapped_RAS.nii.gz: semi-automatically, manually segmented right hypothalamus XXX_MPRAGE_t1_reorient_16bit_acpc_noz0_skullstripped_WarpedToTemplate.nii.gz: T1 warped to intermediate template XXX_MPRAGE_t1_reorient_16bit_acpc_noz0_skullstripped_Warp.nii.gz: warpfield from T1 to intermediate template XXX_MPRAGE_t1_reorient_16bit_acpc_noz0_skullstripped_InverseWarp.nii.gz: inverse warpfield from T1 to intermediate template XXX_MPRAGE_t1_reorient_16bit_acpc_noz0_skullstripped_Affine.txt: affine transform from T1 to intermediate template

#Template T150template0.nii.gz: template originating from N=150 participants of the LIFE-Adult Study