LASHiS

NB This fork is no longer maintained. Please see https://github.com/thomshaw92/LASHiS

Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using multi-contrast MRI.

The publication for this work is available at https://doi.org/10.1016/j.neuroimage.2020.116798

Data for the TOMCAT dataset referenced in this work is located at https://osf.io/bt4ez/

Requirements:

Requires ANTs https://github.com/ANTsX/ANTs/ (>= v2.3.0)

Requires ASHS https://sites.google.com/site/hipposubfields/home

Docker/Singularity image (including LASHiS and all required software)

docker pull caid/lashis_1.0

or

singularity build LASHiS.simg docker://caid/lashis_1.0:latest That can be run with:

singularity exec LASHiS.simg /LASHiS.sh \
		-a atlas selection for ashs \
        	-OptionalArguments \
		-o outputPrefix \
		anatomicalImages (see below for details)

Note that no other environmental variables need to be set, though you will need to specify bind points to your data in Singularity.

If you wish to build the container for reproduction of the ADNI pipeline, please see the directory /Experiment_files_for_LASHiS/Scripts/Singularity/

Google Colab version of LASHiS

https://colab.research.google.com/drive/1rFwEuf_sQk62HPSSxjJffGWLwS_-n_u6?usp=sharing

LASHiS pipeline steps:

LASHiS performs a longitudinal estimation of hippoocampus subfields. The following steps are performed:

1. Run Cross-sectional ASHS on all timepoints
2. Create a single-subject template (SST) from all the data, then cross-sectionally run the SST through ASHS.
3. Using the Cross-sectional inputs as priors, label the hippocampi of the SST.
4. Segmentation results are reverse normalised to the individual time-point.

Environment Variables:

ASHS_ROOT Path to the ASHS root directory

ANTSPATH Path to the ANTs root directory

Misc Notes:

LASHiS was loosely adapted from the ANTs Longitudinal Cortical Thickness pipeline https://github.com/ANTsX/ANTs/ The ASHS_TSE image slice direction should be z. In other words, the dimension of ASHS_TSE image should be 400x400x30 or something like that, not 400x30x400

Usage:

/path/to/LASHiS.sh -a atlas selection for ashs \
    	<OPTARGS> \
	-o outputPrefix \
	\${anatomicalImages[@]} \

Required arguments:

 -o:  Output prefix                         The following subdirectory and images are created for the single
                                            subject template
                                              * \${OUTPUT_PREFIX}SingleSubjectTemplate/
                                              * \${OUTPUT_PREFIX}SingleSubjectTemplate/T_template*.nii.gz
 -a: Atlas selection                        Full path for the atlas you would like to use for the Cross-sectional
                                            labelling of ASHS and the SST. Can be made in ASHS_train
 anatomical images                          Set of multimodal (T1w or gradient echo, followed by T2w FSE/TSE input)
                                            data. Data must be in the format specified by ASHS & ordered as follows:
                                              ${time1_T1w} ${time1_T2w} \
                                              ${time2_T1w} ${time2_T2w} \
                                              .
                                              .
                                              .
                                              ${timeN_T1w} ${timeN_T2w} ...

Optional arguments:

 -c:  control type                          Control for parallel computation for ANTs steps (JLF,SST creation)  (default 0):
                                              0 = run serially
                                              1 = SGE qsub
                                              2 = use PEXEC (localhost) (remember to define cores in -j)
                                              3 = Apple XGrid
                                              4 = PBS qsub
                                              5 = SLURM
 
 -d:  OPTS                                  Pass in additional options to SGE's qsub for ASHS. Requires -c 1

 -e:  ASHS file                             ProConfiguration file. If not passed, uses $ASHS_ROOT/bin/ashs_config.sh 
 -f:  Diet LASHiS                           Diet LASHiS (reverse normalise the SST only) then exit.
 
 -g:  denoise anatomical images             Denoise anatomical images (default = 0).
 -j:  number of cpu cores                   Number of cpu cores to use locally for pexec option (default 2; requires "-c 2")
                                       
 -n:  N4 Bias Correction                    If yes, Bias correct the input images before template creation.
                                            0 = No
                                            1 = Yes
 
 -b:  keep temporary files                  Keep brain extraction/segmentation warps, etc (default = 0).

Data structure if you have already created an SST:

project_base_dir   
│
└───SubjectName_LASHiSSingleSubjectTemplate
│   │
│   │   T_subjectname_fiename0Affine.txt
│   │   T_subjectname_fiename0InverseWarp.nii.gz
│   │   T_subjectname_fiename0Warp.nii.gz
│   │   T_subjectname_fiename2Affine.txt
│   │   T_subjectname_fiename2InverseWarp.nii.gz
│   │   T_subjectname_fiename2Warp.nii.gz
│   │   T_template0.nii.gz
│   │   T_template0_rescaled.nii.gz
│   │   T_template1.nii.gz
│   │   T_template1_rescaled.nii.gz #rescaled to have intensity range of 0-1000
│   │   
│   └───SST_ASHS
│   |	| SST ASHS FILES
|   |	| ...
|   |	
|   │   file021.txt
|   │   file022.txt
|    
|    
└───SubjectName_LASHiS
│   │
│   └───Timepoint_1_0
│   |	│
│   |	└───Timepoint_1_XS_ASHS
│   │
│   └───Timepoint_n_0
│   |	│
│   |	└───Timepoint_n_XS_ASHS
│   │
│   └───LASHiS
│       │   stats.txt 
│       │   labels.nii.gz
│       │   ...
  

Subfield labels

Labels are derived directly from the chosen atlas. Labels values are copied from the atlas package to the LASHiS folder for each participant > check under snaplabels.txt

Subfield label stats

The stats text file is in the LASHiS directory as well, and is arranged in the same order as ASHS: Columns: {side} {subfield name} {number of voxels containing the label} {volume in mm^2} for example:

cat LASHiS/{subjName}{side}SSTLabelsWarpedToTimePoint{timepoint}_stats.txt
left CA1 125 1102.059
left CA2 52 16.497
left DG 111 721.278
left CA3 48 57.375
left misc 58 98.091
left SUB 120 405.837
left ERC 66 461.997
left BA35 75 507.465
left BA36 83 1746.954
left PHC 65 1186.920
left sulcus 134 451.170