kedar-codes / hippo_morph_old

The old, outdated code for my hippocampal morphometry pipeline.

hippo_morph_old

The old, clunky, and outdated code for my hippocampal morphometry pipeline. The scripts located here are for documentation/preservation purposes only and have largely been replaced by my Python-based workflow.

Primarily BASH script-based. Requires hippodeep_pytorch and SlicerSALT.

The intended order of running these scripts goes something like this:

1. SAP_create_project.sh to create a basic directory hierarchy for the project and the various files produced by segmentation, SPHARM-PDM, SlicerSALT modules, etc.

2. SAP_hippodeep_seg.sh for fast, machine learning-based hippocampal (only) segmentation via hippodeep_pytorch or SAP_FS_seg.sh for FreeSurfer-based multi-ROI segmentation. batch_hippodeep_seg.sh is an older version of the former.

3. If using FreeSurfer to segment your T1-weighted images, SAP_extract_ROIs.sh will use FSL's fslmaths tool to extract your segmented volumes (masks) using FreeSurfer's aseg.nii.gz label map.

4. SAP_SPHARM_P920.sh for running SlicerSALT's SPHARM-PDM computation on the newly produced segmentation volumes.

5. batch_model2model_distance.py and SAP_meshmath.py are both ways to interact with SlicerSALT's "Model to Model Distance" module/functionality via command line for batch processing of multiple VTK files. Requires VTK models produced via SPHARM-PDM.

SAP_extract_points.py is not required for the pipeline, but is a script that goes through a directory of VTK models, extracts the Cartesian coordinates of each model's vertices, and saves them to a per-model CSV file. Useful for calculating vectors, visualizing a model as a 3D scatterplot/point cloud in MATLAB, etc.

The MATLAB_scripts folder contains vtk_insula_test.m and SAP_plot_sig_vert.m, as well as a handful of CSV and VTK files. vtk_insula_test.m is a simple demo to visualize the vertices/points of the included L_insula.vtk model as a point cloud/3D scatter plot. SAP_plot_sig_vert.m is meant to identify vertices/points that experienced significant change (via vector data contained in the included CSV files) and highlight them in a point cloud/3D scatter plot using the vertices of a template hippocampus contained in template_vertices.csv. Significance is calculated via a one-sample Wilcoxon signed rank test. SAP_plot_sig_vert.m requires some additional MATLAB toolboxes (Bioinformatics, etc.) to be installed.

Refer to comments in code for detailed directions on running these scripts.