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. |
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] [--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¶
--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. |
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. |
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. |