Outputs of Neurocaps

In neurocaps, functions that produce NifTI images, plots, or dataframes have an output_dir parameter to specify where files should be saved. The file types includes:

  • NifTI images: saved as "nii.gz".

  • Matplotlib, Plotly, & Seaborn plots: saved as "png", and also as "html" if the as_html=True in CAP.caps2radar (which uses Plotly).

  • Pandas Dataframes: saved as "csv".

  • Pickles: saved as "pkl".

All functions have default file names that follow a specific format. Many functions also include parameters to add a prefix (before the default file name) or suffix (after the default file name and before the extension) name.

General File Naming Format

The default file naming convention for the most files produced by the neurocaps.analysis module typically includes:

  1. The group name (if specified, defaults to "All Subjects" if not specified).

  2. The CAP ID (for functions in the CAP class that produce one output per CAP; else, "CAPs" is used).

  3. A descriptor of the file content.

  4. The file extension.

Format for Files Produced by CAP or transition_matrix:

[Group_Name]_[CAP-n]_[descriptor].[extension]

# Or
[Group_Name]_CAPs_[descriptor].[extension]

# Format for Files Produced by CAP.get_caps
[Group_Name]_[clustering_evaluation_metric].[extension]

Examples for Files Produced by CAP or transition_matrix (No Group Specified):

All_Subjects_CAP-1_radar.png

All_Subjects_CAP-1_radar.html

All_Subjects_CAPs_heatmap-nodes.png

All_Subjects_CAPs_correlation_matrix.png

All_Subjects_CAPs_transition_probability_matrix.png

All_Subjects_CAPs_transition_probability_matrix.csv

Examples (With Groups Specified):

In this example, "High ADHD" and "Low ADHD" are used as group names. Note that an underscore is added despite the whitespace in the names:

High_ADHD_davies_bouldin.png

Low_ADHD_variance_ratio.png

High_ADHD_CAP-2.nii.gz

Low_ADHD_CAP-2.nii.gz

High_ADHD_CAP-2_surface.png

Low_ADHD_CAP-2_surface.png

Exceptions to the Default Naming Scheme

Certain methods do not follow the default naming convention. This pertains to TimeseriesExtractor.visualize_bold, TimeseriesExtractor.timeseries_to_pickle. CAP.calculate_metrics, merge_dicts, standardize, and change_dtype.

  • TimeseriesExtractor.visualize_bold - The default name format is as follows (but can be overwritten using the file_name parameter):

subject-[subj_id]_run-[run_id]_timeseries.png

  • TimeseriesExtractor.timeseries_to_pickle - The default name format is as follows (but can be overwritten using the file_name parameter):

subject_timeseries.pkl

  • CAP.calculate_metrics - The naming format generally includes only the metric name (e.g. [metric_name].csv). However, for the "transition_probability" metric, separate dataframes are saved for each group:

persistence.csv

temporal_fraction.csv

counts.csv

transition_frequency.csv

transition_probability-[Group_Name].csv

  • merge_dicts, standardize, and change_dtype - The default name format for each is as follows (but can be overwritten using the file_names parameter):

    • merge_dicts

    subject_timeseries_0_reduced.pkl

subject_timeseries_1_reduced.pkl

merged_subject_timeseries.pkl

    • standardize

    subject_timeseries_0_standardized.pkl

    • change_dtype

    # Format: subject_timeseries_0_dtype-[dtype].pkl
subject_timeseries_0_dtype-float16.pkl