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Short Description
Docker container used for the statistical modeling and inference of the CNP data.
Full Description

CNP task analysis

This repository contains the code to analyse the CNP task data (ds_000030, available on openfmri.org).

Reproducibility

The only dependency to re-run these analyses is singularity 2.3.

The analyses have been run in a singularity container, based on a docker container. The docker container is publicly available on docker hub.

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

The data is assumed to be structured in BIDS format and preprocessed using fmriprep. All configuration (loading singularity, referencing data and code paths) is specified in config.sh.

File structure

+-- 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.
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poldracklab
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