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.

  • Examples 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 by CAP (With Groups Specified)

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.report_qc, 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 filename 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 filename parameter):

subject_timeseries.pkl

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

report_qc.csv

  • 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 filenames 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