Command line interface

graynet 2.0 exposes subcommands for the main run modes and for optional exports. Each successful command writes one run directory containing canonical outputs.

usage: graynet [-h] [-v] {edges,multiedge,roi-stats,export} ...

Positional Arguments

command

Possible choices: edges, multiedge, roi-stats, export

Named Arguments

-v, --version

show program’s version number and exit

Sub-commands

edges

Compute single-feature edge networks.

graynet edges [-h] -i INPUT_DIR [-s SUBJECT_IDS_PATH] [-a ATLAS] [-o OUT_DIR]
              -f FEATURES [-p SMOOTHING_PARAM] [-n NODE_SIZE] [-c NUM_PROCS]
              -w WEIGHT_METHODS [WEIGHT_METHODS ...] [-b NUM_BINS]
              [-e MIN MAX]

Named Arguments

-i, --input-dir
-s, --subjects
-a, --atlas
-o, --out-dir
-f, --feature

Feature name(s) to process.

-p, --smoothing-param
-n, --node-size
-c, --num-procs
-w, --weight
-b, --num-bins
-e, --edge-range

multiedge

Compute multi-feature edge networks.

graynet multiedge [-h] -i INPUT_DIR [-s SUBJECT_IDS_PATH] [-a ATLAS]
                  [-o OUT_DIR] -f FEATURES [FEATURES ...] [-p SMOOTHING_PARAM]
                  [-n NODE_SIZE] [-c NUM_PROCS] -w WEIGHT_METHODS
                  [WEIGHT_METHODS ...] [-b NUM_BINS]
                  [-t SUMMARY_STATS [SUMMARY_STATS ...]]
                  [-l [MULTI_EDGE_RANGE ...]]

Named Arguments

-i, --input-dir
-s, --subjects
-a, --atlas
-o, --out-dir
-f, --feature

Feature name(s) to process.

-p, --smoothing-param
-n, --node-size
-c, --num-procs
-w, --weight
-b, --num-bins
-t, --summary-stat
-l, --multi-edge-range

Pairs of min/max values, one pair per feature.

roi-stats

Compute ROI summary statistics.

graynet roi-stats [-h] -i INPUT_DIR [-s SUBJECT_IDS_PATH] [-a ATLAS]
                  [-o OUT_DIR] -f FEATURES [-p SMOOTHING_PARAM] [-n NODE_SIZE]
                  [-c NUM_PROCS] -r ROI_STATS [ROI_STATS ...]

Named Arguments

-i, --input-dir
-s, --subjects
-a, --atlas
-o, --out-dir
-f, --feature

Feature name(s) to process.

-p, --smoothing-param
-n, --node-size
-c, --num-procs
-r, --roi-stat

export

Export canonical outputs to other formats.

graynet export [-h] {graphml,csv} ...

Positional Arguments

export_command

Possible choices: graphml, csv

Sub-commands

graphml

Export GraphML files from a run.

graynet export graphml [-h] --run-dir RUN_DIR [--out-dir OUT_DIR]
Named Arguments
--run-dir
--out-dir
csv

Export CSV files from a run.

graynet export csv [-h] --run-dir RUN_DIR [--out-dir OUT_DIR]
Named Arguments
--run-dir
--out-dir

Single-feature edge extraction

graynet edges \
  -i /work/project/freesurfer_reconall \
  -s subject_ids.txt \
  -f freesurfer_thickness \
  -w manhattan euclidean \
  -a fsaverage \
  -p 10 \
  -o /work/project/graynet_runs \
  -c 2

Multi-edge extraction

graynet multiedge \
  -i /work/project/freesurfer_reconall \
  -s subject_ids.txt \
  -f freesurfer_thickness freesurfer_curv \
  -w manhattan \
  -t median prod \
  -a fsaverage \
  -p 10 \
  -o /work/project/graynet_runs

ROI-wise statistics

graynet roi-stats \
  -i /work/project/freesurfer_reconall \
  -s subject_ids.txt \
  -f freesurfer_thickness \
  -r median mean \
  -a fsaverage \
  -p 10 \
  -o /work/project/graynet_runs

Exporting GraphML or CSV

Canonical outputs are Parquet plus JSON metadata. Export GraphML or CSV only when you need those downstream formats.

graynet export graphml --run-dir /work/project/graynet_runs/edges__atlas-fsaverage__features-freesurfer_thickness__weights-manhattan__smth-10__node-none

graynet export csv --run-dir /work/project/graynet_runs/edges__atlas-fsaverage__features-freesurfer_thickness__weights-manhattan__smth-10__node-none