A BrainHack Project to compare thickness outputs from different pipelines run on ABIDEI
The principle deliverables of this project are:
- a set of unified data tables for FreeSurfer (version 5.1 and 5.3) and ANTS anatomic analyses of the ABIDE 1 data, and
- 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
dplyr. The latest versions of these libraries come packaged together inside the "tidyverse" can be installed with:
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