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Cortical Thickness - Folder Structure

bin/

This folder includes:

  • All the third-party executables used by this project.
  • Python Environment called pyenv and the requirements.txt.

lib/

This folder includes third-party libraries.

share/

This folder includes resources used by the scripts such as templates and transform files.

code/

This folder includes all the scripts made for this project.

code/corticalThickness.py

Script useful to parse cmd line args for Cortical Thickness pipeline.

code/corticalThicknessDocker.py

Script useful to parse cmd line args for Cortical Thickness pipeline using Docker Image.

code/SKELETON-pipeline-0.1.bash

Main Script, It includes all the steps of the pipeline, mainly focused in the CP outer boundary extraction using homotopic skeletonization method, but it also calls/uses the surface extractions scripts.

code/WHITE-EXTRACTION.bash

Script useful for white matter surface extraction.

code/SURFACE-EXTRACTION.bash

Script useful for gray matter surface extraction expanding WM till the Skeleton extracted previously.

code/skeleton

This folder includes all the python scripts made to build a homotopic skeleton of the cortical plate.

code/skeleton/align_nii.py

Script useful to align two nii files to the same center.

code/skeleton/FCM.py

Fuzzy C Means, Soft Clustering. General Implementation Class

code/skeleton/MRI_FCM.py

Fuzzy C Means, Soft Clustering. Usign FCM.py for MRI intensity segmentation purpose.

code/skeleton/sFCM.py

Fuzzy Spatial C Means, Soft Clustering. General Implementation Class

code/skeleton/MRI_sFCM.py

Fuzzy Spatial C Means, Soft Clustering. Usign sFCM.py for MRI intensity segmentation purpose.

code/skeleton/GMM.py

Gaussian Mixture Model, Soft Clustering CSF/GM considering intensity.

code/skeleton/pial_surface.py

Pial Surface extraction (inner boundary of CSF) expanding White Matter till CSF.

code/surfaceExtraction/analyzeTxt.py

Script useful to analyze data (RMS, Average, Std dev, Min, Max) enlisted in a txt file.

code/surfaceExtraction/expand_from_white_fetal.pl

Script capable of expanding white matter obj till laplacian field for cp surface extraction.

code/surfaceExtraction/laplace.pl

Script that generates a laplacian field for Cortica Plate given its volume file.

code/utils/convertmnc.bash

Script that converts all mnc files of a given path to nii.

code/utils/morphometrics.bash

Script that calculates cortical thickness using three different methods.

code/utils/openfreeviewResults.bash

Script that opens in freeeview all important files of a given case.

code/utils/runAnalysis.bash

Script that run analyzeTxt.py for all txt files inside a folder (recursively).

code/utils/runPipelineSamples.bash

Script that run the current pipeline for all cases in Samples folder.

code/utils/runPipelineSamples.bash

Script that run the surface extraction for all cases in Samples folder.

deploy/

This folder includes all files related to docker deployment.

deploy/cmds.md

File with indications about Docker.

deploy/Dockerfile

File with instructions to build a docker image.

deploy/runBash.sh

Script to create a docker container using cortical-thickness image.

deploy/runScript.sh

Script to call the pipeline using docker container.

refs/

This folder includes useful technical resources for the understading of the project.

refs/Pipeline_Overview.pdf

Slides explaining each step of the pipeline.

refs/ProyectProposal.pdf

Background Knowledge about the project and the goal of this pipeline in it.

refs/spatialFuzzyC.pdf

Technical Paper used for the development of sFCM (spatial Fuzzy Clustering Method).

refs/VipSkeleton.txt

Command Arguments of the executable capable of making the homotopic skeleton.