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Aug 8, 2018
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DOC: Example model #63

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DOC: Update help in README
effigies Aug 6, 2018
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DOC: Add example model, link to others
effigies Aug 6, 2018
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DOC: Note syntax
effigies Aug 6, 2018
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124 changes: 121 additions & 3 deletions README.rst
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Expand Up @@ -17,8 +17,10 @@ See the output of ``fitlins --help`` for all valid options::

usage: fitlins [-h] [-v]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-m MODEL] [-p PREPROC_DIR] [--space {MNI152NLin2009cAsym}]
[--debug]
[-m MODEL] [-p PREPROC_DIR]
[--derivative-label DERIVATIVE_LABEL]
[--space {MNI152NLin2009cAsym}] [--include INCLUDE]
[--exclude EXCLUDE] [--n-cpus N_CPUS] [--debug] [-w WORK_DIR]
bids_dir output_dir {run,session,participant,dataset}

FitLins: Workflows for Fitting Linear models to fMRI
Expand All @@ -40,18 +42,132 @@ See the output of ``fitlins --help`` for all valid options::
-m MODEL, --model MODEL
location of BIDS model description (default bids_dir/model.json)
-p PREPROC_DIR, --preproc-dir PREPROC_DIR
location of preprocessed data (default output_dir/fmriprep)
location of preprocessed data (if relative path, search
bids_dir/derivatives, followed by output_dir)
--derivative-label DERIVATIVE_LABEL
execution label to append to derivative directory name
--space {MNI152NLin2009cAsym}
registered space of input datasets
--include INCLUDE regex pattern to include files
--exclude EXCLUDE regex pattern to exclude files

Options to handle performance:
--n-cpus N_CPUS maximum number of threads across all processes
--debug run debug version of workflow

Other options:
-w WORK_DIR, --work-dir WORK_DIR
path where intermediate results should be stored

At present, FitLins does not support smoothing or operate in subject-native
space.
It is developed against `FMRIPREP`_-preprocessed datasets, but is intended to
work with any dataset following the `BIDS Derivatives`_ draft specification.

Models
------

By default, FitLins will look for a ``model.json`` in the root of the BIDS
directory.
A simple example model for `OpenFMRI dataset ds000030`_ is reproduced below::


{
"name": "ds000030_bart",
"description": "model for balloon analog risk task",
"input": {
"task": "bart"
},
"blocks": [
{
"level": "run",
"transformations": [
{
"name": "factor",
"input": [
"trial_type",
"action"
]
},
{
"name": "and",
"input": [
"trial_type.BALOON",
"action.ACCEPT"
],
"output": [
"accept"
]
},
{
"name": "and",
"input": [
"trial_type.BALOON",
"action.EXPLODE"
],
"output": [
"explode"
]
}
],
"model": {
"HRF_variables":[
"accept",
"explode"
],
"variables": [
"accept",
"explode",
"FramewiseDisplacement",
"X",
"Y",
"Z",
"RotX",
"RotY",
"RotZ"
]
},
"contrasts": [
{
"name": "accept_vs_explode",
"condition_list": [
"accept",
"explode"
],
"weights": [1, -1],
"type": "T"
}
]
},
{
"level": "dataset",
"model": {
"variables": [
"accept_vs_explode"
]
},
"contrasts": [
{
"name": "group_accept_vs_explode",
"condition_list":[
"accept_vs_explode"
],
"weights": [1],
"type": "T"
}
]
}
]
}

Additional examples can be found in the `models`_ branch of the main FitLins
repository.

.. note::

The BIDS Model specification is a draft standard, and some details may
change over time.

Warning
-------

Expand All @@ -65,3 +181,5 @@ The command-line interface outlined above should be fairly stable, however.
.. _`BIDS Derivatives`: https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/
.. _BIDS-Apps: http://bids-apps.neuroimaging.io
.. _FMRIPREP: https://fmriprep.readthedocs.io
.. _`OpenFMRI dataset ds000030`: http://datasets.datalad.org/?dir=/openfmri/ds000030/
.. _models: https://github.com/poldracklab/fitlins/tree/models
0