CLI Reference¶

QSIParc exposes a single command: qsiparc.

Synopsis¶

qsiparc [OPTIONS] QSIRECON_DIR OUTPUT_DIR

Arguments¶

Argument	Description
`QSIRECON_DIR`	Path to the QSIRecon derivatives directory. Must exist.
`OUTPUT_DIR`	Path to write QSIParc outputs. Created if it does not exist.

Options¶

Filtering¶

Option	Short	Type	Default	Description
`--participant-label`	`-p`	`str`	all subjects	Process a single subject. Accepts `sub-001` or `001`.
`--session-label`	`-s`	`str`	all sessions	Process a single session. Accepts `ses-01` or `01`.
`--atlas`	`-a`	`str` (repeatable)	all atlases	Restrict to one or more atlases by name. Repeatable: `-a 4S156Parcels -a 4S256Parcels`.
`--scalars`		`str` (repeatable)	all discovered	Scalar names to extract. Repeatable: `--scalars FA --scalars MD`.

Processing¶

Option	Type	Default	Description
`--stat-tier`	choice	`extended`	Statistic tier. One of `core`, `extended`, `diagnostic`, `all`.
`--zero-is-missing`	flag	off	Treat voxels with value `0.0` as missing data (NaN) during extraction. Useful for masked diffusion maps where background = 0.

Execution¶

Option	Short	Type	Default	Description
`--dry-run`		flag	off	List what would be processed without actually running.
`--verbose`	`-v`	count	0 (WARNING)	Increase verbosity. `-v` → INFO, `-vv` → DEBUG.

Examples¶

# All subjects, all atlases, default settings
qsiparc /data/qsirecon /data/qsiparc-out

# Single subject with INFO logging
qsiparc /data/qsirecon /data/qsiparc-out \
    --participant-label sub-001 \
    -v

# Single subject, single session, debug logging
qsiparc /data/qsirecon /data/qsiparc-out \
    --participant-label sub-001 \
    --session-label ses-01 \
    -vv

# Single atlas
qsiparc /data/qsirecon /data/qsiparc-out \
    --atlas Schaefer2018N100Tian2020S2

# Multiple atlases
qsiparc /data/qsirecon /data/qsiparc-out \
    -a 4S156Parcels \
    -a 4S256Parcels \
    -a Schaefer2018N100Tian2020S2

# Only specific scalar maps
qsiparc /data/qsirecon /data/qsiparc-out \
    --scalars FA \
    --scalars MD \
    --scalars ICVF

# Treat zeros as missing data (common for masked diffusion maps)
qsiparc /data/qsirecon /data/qsiparc-out --zero-is-missing

# Dry run: see what would be processed
qsiparc /data/qsirecon /data/qsiparc-out --dry-run

Exit codes¶

Code	Meaning
`0`	All parcellations succeeded
`1`	Partial failure — some subjects/atlases failed, others succeeded
`2`	Total failure — no successful outputs

Logging format¶

HH:MM:SS [LEVEL  ] module | message

Each log message includes the module name for easy filtering. At INFO level, every extracted scalar and written file is logged. At DEBUG level, full subprocess commands are printed.

Stat tiers¶

The --stat-tier option controls which columns appear in the output TSV:

Tier	Columns included
`core`	`mean`
`extended`	`mean`, `median`, `std`, `iqr`, `skewness`, `kurtosis`, `n_voxels`, `coverage`
`diagnostic`	All extended + additional diagnostic metrics
`all`	Everything available

The default extended tier provides the full set described in the Output Format specification.