CNP task analysis
This repository contains the code to analyse the CNP task data (ds_000030, available on openfmri.org).
The only dependency to re-run these analyses is singularity 2.3.
On a machine that has docker installed, the singularity container can be obtained by running:
docker run -v /var/run/docker.sock:/var/run/docker.sock -v /local:/output --privileged -t --rm singularityware/docker2singularity poldracklab/cnp_task_analysis:1.0
After running this command, the singularity container can be found in the
/local folder on the local machine.
Machine and data configuration
+-- hpc/ Folder with scripts used to submit and run jobs | | on a HPC environment with a SLURM scheduler. | | | +-- 01_prepare.sh Script to prepare task files (each line = 1 task) | +-- 02_CNP_analysis.sh Array job script that run the first level analyses. | +-- 03_CNP_2nd_level.sh Array job script that runs the group analyses. | +-- 04_CNP_2nd_level_ACM.sh Job script to compute the ACM's for all contrasts. | | | +-- write_contrasts.py Python script to write json with contrast information. | | (called by 01_prepare.sh) | +-- write_tasks.py Python script to write task files. | | (called by 01_prepare.sh) | +-- write_group_tasks.py Python script to write task files. | (called by 01_prepare.sh) +-- utils/ | +-- utils.py Functions used in first level analyses. | +-- rename_copes.py Script to rename and collect the tmaps for neurovault. | +-- CNP_analysis.py Program to run first level analysis on 1 subject. +-- CNP_2nd_level.py Program to run group level analysis on 1 contrast | (and 1 task). +-- CNP_2nd_level_ACM.py Program to generate ACM's for all contrasts. +-- CNP_group_figures.py Program to write figures used in the accompanying | paper. +-- config.sh configuration file setting environment variables | specifying the location of the data and code. +-- Dockerfile File to create docker container. Autobuild on docker hub.