.. include:: links.rst
.. _Usage :
Usage Notes
===========
.. warning::
*sMRIPost-LINC* requires preprocessing outputs in MNI152NLin6Asym space with
2 mm3 voxels (i.e., ``res-02``).
Make sure you run fMRIPrep with ``--output-spaces MNI152NLin6Asym:res-02``.
.. warning::
*sMRIPost-LINC* includes a tracking system to report usage statistics and errors
for debugging and grant reporting purposes.
Users can opt-out using the ``--notrack`` command line argument.
Execution and the BIDS format
-----------------------------
The *sMRIPost-LINC* workflow takes as principal input the path of the dataset
that is to be processed.
The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data
Structure)` format, and it must include at least one T1w structural image and
(unless disabled with a flag) a BOLD series.
We highly recommend that you validate your dataset with the free, online
`BIDS Validator `_.
The exact command to run *sMRIPost-LINC* depends on the Installation_ method.
The common parts of the command follow the `BIDS-Apps
`_ definition.
Example: ::
smripost_linc data/bids_root/ out/ participant -w work/
Further information about BIDS and BIDS-Apps can be found at the
`NiPreps portal `__.
Command-Line Arguments
----------------------
.. argparse::
:ref: smripost_linc.cli.parser._build_parser
:prog: smripost_linc
:nodefault:
:nodefaultconst:
.. _prev_derivs:
Reusing precomputed derivatives
-------------------------------
Reusing a previous, partial execution of *sMRIPost-LINC*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*sMRIPost-LINC* will pick up where it left off a previous execution, so long as the work directory
points to the same location, and this directory has not been changed/manipulated.
Some workflow nodes will rerun unconditionally, so there will always be some amount of
reprocessing.
Troubleshooting
---------------
Logs and crashfiles are output into the
``