CONP Portal | FreeSurfer-Stats2table


Run Locally Using Boutiques
Boutiques
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Run on the CBRAIN Platform
Online platform
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Run on HPCs with Clowdr
Compute Canada
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Author:

Laboratory for Computational Neuroimaging

Description:

Converts a stats file created by recon-all into a table in which each line is a subject and each column is a parcellation (command: aparcstats2table) or segmentation (command: asegstats2table): https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table, https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table.

Container Image:

index: docker://

image: freesurfer/freesurfer:7.1.1

type: singularity

Instructions

How to run the tool locally

CONP pipelines can be easily installed and run on any computer wth a container engine. The preferred container for the tool is available in the Container Image field above. For detailed information on how to use Boutiques, please visit this tutorial.

1. List the inputs/outputs needed for the pipeline to run

Note: this command will list only the required options to run the pipeline. To view the complete list of options, use

bosh example --complete zenodo.8033560

2. Create an invocation JSON file based on the output of the bosh example

3. Run the pipeline with the invocation JSON file created in 2.

Note: the option -s will show STDERR, STDOUT in the terminal. The option -v allows mounting a directory from your system onto the container engine.