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README.md

compare_surf_tools

A BrainHack Project to compare thickness outputs from different pipelines run on ABIDEI

The principle deliverables of this project are:

  1. a set of unified data tables for FreeSurfer (version 5.1 and 5.3) and ANTS anatomic analyses of the ABIDE 1 data, and
  2. a set of R analysis scripts that reads and performs simple comparison analyses on these data tables.

The Data Files

Consolidated from the analysis results provided at http://preprocessed-connectomes-project.org/abide/Description, we provide the following unified data tables in the 'data' directory:

  • ABIDE_Phenotype.csv ! phenotypic data for the subjects
  • ABIDE_ants_thickness_data.csv ! thickness data from ANTS analysis
  • ABIDE_fs5.3_LandRvolumes.csv ! volume data from FreeSurfer 5.3 analysis
  • ABIDE_fs5.3_thickness.csv ! thickness data from FreeSurfer 5.3 analysis
  • abide_fs5.1_landrvolumes.csv ! volume data from FreeSurfer 5.1 analysis
  • cortical_fs5.1_measuresenigma_thickavg.csv ! thickness data from FreeSurfer 5.1 analysis
  • subject_check.csv ! summary table of the data available per subject

The R Scripts

Description of the R Scripts...

In the 'analysis' diretory, there are R the following R scripts:

  • abide_ct.R ! Script to...
  • data_prep.R ! Script to Combine the data sources into one merged data frame with some added labels for grouping the results by hemisphere, lobe, etc.
  • heatmap_plot.R ! Script to check possible mis-alignment of label names
  • pairs_plot.R ! Script to create tool-pair plots with scatterplot in lower triangle, histograms on main diagonal, and correlation coefficients (Pearson) on the upper diagonal.

There are also Rmd scripts in this directory:

  • double_check.Rmd ! A script to double check that the ROIs at least matched up in the same way across the data sources.
  • dx_effect_testing.Rmd ! Script to look at diagnostic effects in the thickness data.

In the 'bin' directory, there is the following Rmd script:

  • LandRvolumes_comparison.Rmd ! Script to...

R package requirements

Some of the scripts here make use of R libraries ggplot2, tidyr and dplyr. The latest versions of these libraries come packaged together inside the "tidyverse" can be installed with:

install.packages(tidyverse)

R markdown

Some of these sciprts are written in rmardown, which can be quickly converted in to html or pdf reports. The libararies for working with R markdown come packaged within the Rstudio IDE, so anybody using it should have them already. Click here for more info on R markdown. We provide the R markdown scripts and also the rendered .pdf reports in this repo.

If not using Rstudio. You will need the following libraries to render the .rmd file into and .html report

install.packages(knitr)
install.packages(rmarkdown)
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