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DOC: Update README with latest help text, remove smoothing disclaimer #119

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merged 4 commits into from
Mar 4, 2019
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DOC: Update README with latest help text, remove smoothing disclaimer #119

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8175f9c
Update README.rst
kfinc Mar 4, 2019
021ac73
Update README.rst
kfinc Mar 4, 2019
c941d91
fixed spacing issues
kfinc Mar 4, 2019
31e5635
DOC: Re-run fitlins --help + minor cleanups
effigies Mar 4, 2019
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14 changes: 8 additions & 6 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,9 @@ See the output of ``fitlins --help`` for all valid options::
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-m MODEL] [-p PREPROC_DIR]
[--derivative-label DERIVATIVE_LABEL]
[--space {MNI152NLin2009cAsym}] [--include INCLUDE]
[--exclude EXCLUDE] [--n-cpus N_CPUS] [--debug] [-w WORK_DIR]
[--space {MNI152NLin2009cAsym}] [-s --smoothing]
[--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 Down Expand Up @@ -48,6 +49,9 @@ See the output of ``fitlins --help`` for all valid options::
execution label to append to derivative directory name
--space {MNI152NLin2009cAsym}
registered space of input datasets
-s --smoothing full width at half-maximum (FWHM) mm kernel
(valid types: iso (isotropic); e.g. `--smothing iso:5` will use
an isotropic 5mm FWHM kernel)
--include INCLUDE regex pattern to include files
--exclude EXCLUDE regex pattern to exclude files

Expand All @@ -59,10 +63,8 @@ See the output of ``fitlins --help`` for all valid 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.
At present, FitLins does not 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.
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Can you just modify the first sentence? I use newlines after each sentence to reduce the diff when sentence length cascades to line changes, as it does here.

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Thanks! How about now?


Models
------
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