Command Line Interface¶
NiMARE provides several workflows as command-line interfaces, including ALE meta-analysis, meta-analytic coactivation modeling (MACM) analysis, peaks2maps image reconstruction, 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,conperm,peaks2maps,macm,scale,metacluster,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
conperm¶
Meta-analysis of contrast maps using random effects and two-sided inference with empirical (permutation-based) null distribution and Family Wise Error multiple comparisons correction. Input may be a list of 3D files or a single 4D file.
nimare conperm [-h] [--mask FILE] [--output_dir PATH] [--prefix PREFIX]
[--n_iters N_ITERS]
FILE [FILE ...]
Positional Arguments¶
- FILE
Data to analyze. May be a single 4D file or a list of 3D files.
Named Arguments¶
- --mask
Mask file.
- --output_dir
Output directory.
Default: “.”
- --prefix
Common prefix for output maps.
Default: “”
- --n_iters
Number of iterations for permutation testing.
Default: 10000
peaks2maps¶
Method for performing coordinate-based meta-analysis that uses a pretrained deep neural network to reconstruct unthresholded maps from peak coordinates. The reconstructed maps are evaluated for statistical significance using a permutation-based approach with Family Wise Error multiple comparison correction.
nimare peaks2maps [-h] [--output_dir PATH] [--prefix PREFIX]
[--n_iters N_ITERS]
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: “”
- --n_iters
Number of iterations for permutation testing.
Default: 10000
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
scale¶
Method for performing Specific CoActivation Likelihood Estimation (SCALE), a modified meta-analytic coactivation modeling (MACM) that takes activation frequency bias into account, for delineating distinct core networks of coactivation, using a permutation-based approach.
nimare scale [-h] [--baseline BASELINE] [--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¶
- --baseline
Voxel-wise baseline activation rates.
- --output_dir
Output directory.
Default: “.”
- --prefix
Common prefix for output maps.
Default: “”
- --n_iters
Number of iterations for permutation testing.
Default: 2500
- --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
metacluster¶
Method for investigating recurrent patterns of activation across a meta-analytic dataset, thus identifying trends across a collection of experiments.
nimare metacluster [-h] [--output_dir PATH] [--prefix PREFIX]
[--kernel {ALEKernel,MKDAKernel,KDAKernel,Peaks2MapsKernel}]
[--algorithm {kmeans,dbscan,spectral}] --clust_range
CLUST_RANGE CLUST_RANGE (--coord | --img)
dataset_file
Positional Arguments¶
- dataset_file
Dataset file to analyze.
Named Arguments¶
- --output_dir
Output directory.
Default: “.”
- --prefix
Common prefix for output maps.
Default: “”
- --kernel
Possible choices: ALEKernel, MKDAKernel, KDAKernel, Peaks2MapsKernel
Kernel estimator, for coordinate-based metaclustering.
Default: “ALEKernel”
- --algorithm
Possible choices: kmeans, dbscan, spectral
Clustering algorithm to be used, from sklearn.cluster.
Default: “kmeans”
- --clust_range
Select a range for k over which clustering solutions will be evaluated (e.g., 2 10 will evaluate solutions with k = 2 clusters to k = 10 clusters).
- --coord
Is input data coordinate-based?
Default: False
- --img
Is input data image-based?
Default: False
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.