Command Line Interface
NiMARE provides several workflows as command-line interfaces, including ALE meta-analysis, meta-analytic coactivation modeling (MACM) analysis, and contrast map meta-analysis. Each workflow should generate a boilerplate paragraph with details about the workflow and citations that can be used in a manuscript.
To use NiMARE from the command line, open a terminal window and type:
nimare --help
This will print the instructions for using the command line interface in your command line.
usage: nimare [-h] {ale,macm,sleuth2nimare,neurosynth2nimare} ...
Sub-commands
ale
Run an activation likelihood estimation (ALE) meta-analysis on a Sleuth text file. ALE is a permutation-based meta-analysis of coordinates that uses 3D Gaussians to model activation.
nimare ale [-h] [--output_dir PATH] [--prefix PREFIX] [--file2 SLEUTH_FILE2]
[--n_iters N_ITERS] [--v_thr V_THR] [--fwhm FWHM]
[--n_cores N_CORES]
sleuth_file
Positional Arguments
- sleuth_file
Sleuth text file to analyze.
Named Arguments
- --output_dir
Output directory.
Default: “.”
- --prefix
Common prefix for output maps.
Default: “”
- --file2
Optional second Sleuth file for subtraction analysis.
- --n_iters
Number of iterations for permutation testing.
Default: 10000
- --v_thr
Voxel p-value threshold used to create clusters.
Default: 0.001
- --fwhm
Override sample size-based kernel determination with a single FWHM (in mm) applied to all experiments. Useful when sample size is not available for all data.
- --n_cores
Number of processes to use for meta-analysis. If -1, use all available cores.
Default: 1
macm
Run a meta-analytic coactivation modeling (MACM) analysis using activation likelihood estimation (ALE) on a NiMARE dataset file and a target mask.
nimare macm [-h] --mask MASK_FILE [--output_dir PATH] [--prefix PREFIX]
[--n_iters N_ITERS] [--v_thr V_THR] [--n_cores N_CORES]
dataset_file
Positional Arguments
- dataset_file
Dataset file to analyze.
Named Arguments
- --mask, --mask_file
Mask file
- --output_dir
Output directory.
Default: “.”
- --prefix
Common prefix for output maps.
Default: “”
- --n_iters
Number of iterations for permutation testing.
Default: 10000
- --v_thr
Voxel p-value threshold used to create clusters.
Default: 0.001
- --n_cores
Number of processes to use for meta-analysis. If -1, use all available cores.
Default: 1
sleuth2nimare
Convert a Sleuth text file to a NiMARE json file.
nimare sleuth2nimare [-h] text_file out_file
Positional Arguments
- text_file
Sleuth text file to convert.
- out_file
Output file.
neurosynth2nimare
Convert a Neurosynth text file to a NiMARE json file.
nimare neurosynth2nimare [-h] [--annotations_file FILE] text_file out_file
Positional Arguments
- text_file
Neurosynth text file to convert.
- out_file
Output file.
Named Arguments
- --annotations_file
Optional annotations (features) file.