Code repository to generate results for:

B Caldairou, N Foit, et al. "An MRI-Based Machine Learning Prediction Framework to Lateralize Hippocampal Sclerosis in Patients With Temporal Lobe Epilepsy". Neurology (2021); DOI: 10.1212/WNL.0000000000012699

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1. Software Dependencies

Software dependencies include:

• The minc toolkit: https://bic-mni.github.io/
• CMRep: https://github.com/pyushkevich/cmrep
• QHull: http://www.qhull.org/download/
• SurfStat MATLAB Toolbox: https://www.math.mcgill.ca/keith/surfstat/

CMRep and QHull are used together to generate the skeleton from the subfield labels.

SurfStat is used to read minc volumes, surfaces and .txt feature files in MATLAB.

Pre-processing (non-uniformity correction, registration to MNI space, inter-modality co-registration) can be performed using FreeSurfer, FSL or any other MRI processing pipeline.

Subfield segmentation can be performed through FreeSurfer or ASHS. Best alternative to SurfPatch is to use ASHS with our publicly available manual subfield labels (http://fcon_1000.projects.nitrc.org/indi/retro/mni_hipposeg.html).

Outer surface extraction and parameterization can be performed through the SPHARM extension of 3D Slicer. Binaries are available at: https://www.nitrc.org/projects/spharm-pdm

Main parameters are:

• Subdivision level: 32 for CA, 24 for SUB and DG
• SPHARM degree: 32 for CA, 24 for SUB and DG
• Surface templates are provided - based on the manual segmentation protocol described in:

  Kulaga-Yoskovitz, J. et al., Scientific Data, 2015

• We also provide SPHARM orientation examples (surface_template_for_SPHARM/examples) in order to orient the spherical parameters in a similar manner than ours.

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2. Directory Organization

The assumed organization of the directories is specified below:

- One directory to store the surfaces and the resulting skeletons
	(One directory per case, per side and per subfield)
	[surface_directory]
	|
	|-- TLE_0362_1_L_CA.obj
	|-- TLE_0362_1_L_CA_inter.obj
	|-- TLE_0362_1_L_CA_skelFinal.obj
	|
	|-- TLE_0362_1_L_SUB.obj
	|-- TLE_0362_1_L_SUB_inter.obj
	|-- TLE_0362_1_L_SUB_skelFinal.obj

- One directory to store feature images 
	[image_directory]
	|
	|-- TLE_0362_1_t2cor-0.4_stx_norm-0.4.mnc
	|-- TLE_0362_1_t2wt1wratio_final.mnc
	|-- TLE_0362_1_Brainclass.mnc
	|-- TLE_0362_1_T2norm.mat
	|-- TLE_0362_1_Ventricle.mnc

- One directory to store the txt files resulting from the
	intersection between the blades and the images
	[feature_directory]
	|
	|-- TLE_0362_1_L_CA_ColVol.txt
	|-- TLE_0362_1_R_CA_ColVol.txt
	|-- TLE_0362_1_L_CA_nnt2.txt
	|-- TLE_0362_1_R_CA_nnt2.txt
	|-- TLE_0362_1_L_CA_t2wt1wratio.txt
	|-- TLE_0362_1_R_CA_t2wt1wratio.txt

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3. Blade Extraction

The script is used in the following way (we recommend using the nomenclature stated above):

./get_medial_surface \
	${subfield_surface} \
	${subfield_volume} \
	${individual_output_prefix} # Example: ${SurfaceDirectory}/TLE_0362_1_L_CA

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4. Feature Extraction

This script intersects blade surfaces with volumetric images and computes the columnar volume:

./get_individual_features.sh \
	${prefix} \ # e.g. TLE
	${id} \     # e.g. 0362_1
	${subfield} # CA, SUB or DG
	${side}     # L or R
	${surface_directory} \ # The same described in directory organization
	${image_directory} \
	${feature_directory}

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5. Lateralization

The following series of script can be executed in order to accomplish various tasks:

A_GetTrainingData.m	loads training data and control data set
B_StatisticalStudy.m	performs a statistical study between controls and training data set
C_Validation_TrainingSet.m	performs the nested repeated 5-Fold validation based on the training set
D_Validation_TestSet.m	performs the repeated validation on a separated the test set for generalizability
E_Train_Model.m	performs the training of a final model
F_Test_Individual.m	loads saved training model and ROI (data/final_models_and_ROI.mat), and performs individual lateralization

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License

Copyright 2021 Neuroimaging of Epilepsy Laboratory, McGill University