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Export of FSL statistical results using NIDM as specified at http://nidm.nidash.org/specs/nidm-results.html.

Project description

NIDM-Results for FSL

Build Status

Export mass-univariate neuroimaging results computed in FSL (using FEAT) as NIDM-Results packs.

A NIDM-Results pack is a compressed file containing a NIDM-Results serialization and some or all of the referenced image data files in compliance with NIDM-Results specification.

Usage
usage: nidmfsl [-h] [-g GROUP_NAME NUM_SUBJECTS] [-o OUTPUT_NAME] [-d]
               [-n NIDM_VERSION] [--version]
               feat_dir

NIDM-Results exporter for FSL Feat.

positional arguments:
  feat_dir              Path to feat directory.

optional arguments:
  -h, --help            show this help message and exit
  -g GROUP_NAME NUM_SUBJECTS, --group GROUP_NAME NUM_SUBJECTS
                        Group label followed by number of subjects
  -o OUTPUT_NAME, --output_name OUTPUT_NAME
                        Name of the output. A ".nidm.zip" or ".nidm" (when -d
                        is used) suffix will be appended.
  -d, --directory-output
                        Produces a .nidm directory rather than a .nidm.zip
                        file.
  -n NIDM_VERSION, --nidm_version NIDM_VERSION
                        NIDM-Results version to use (default: latest).
  --version             show program's version number and exit
Installation

To install, run the below command in the bash terminal.

    pip install nidmfsl
Compatible with

FSL version 5.0.9

Testing
Requirements

To run the tests for this repository, the following must be installed

  • Git LFS. Installation instructions for Git LFS can be found here.

  • The python packages vcr and ddt. These can be installed using the below commands in the bash terminal:

pip install vcrpy
pip install ddt

In addition, the test data must also be downloaded from the nidmresults-examples repository to <path_to_this_repository>/test/data/nidmresults-examples.

git lfs clone https://github.com/incf-nidash/nidmresults-examples.git <path_to_this_repository>/test/data/nidmresults-examples
Running the tests

The below command can be used to generate the test cases.

python <path_to_this_repository>/test/export_test_battery.py

Folowing this, the test cases can be verified against the ground truth provided in the nidmresults-examples repository using the below command.

cd <path_to_this_repository>/test/
python -m unittest discover

Project details


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