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README.rst

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@@ -23,8 +23,8 @@ Contents
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- `Help`_
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- `Installation`_
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- `Tutorial`_
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- `Run separate commands`_
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- `Run one command`_
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- `Run separate commands`_
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- `Visualize output`_
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- `Appendix: processing`_
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- `Appendix: output`_
@@ -114,6 +114,19 @@ You would then copy and paste the corresponding address into your web browser
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(in this case, ``http://127.0.0.1:8888/?token=62853787e0d6e180856eb22a51609b25e``),
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and click on "mindboggle_tutorial.ipynb".
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------------------------------------------------------------------------------
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_`Run one command`
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------------------------------------------------------------------------------
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The Mindboggle Docker container can be run as a single command to process
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a T1-weighted MR brain image through FreeSurfer, ANTs, and Mindboggle.
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Skip to the next section if you wish to run ``recon-all``,
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``antsCorticalThickness.sh``, and ``mindboggle`` differently::
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docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID
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Outputs are stored in $DOCK/mindboggle123_output/ by default,
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but you can set a different output path with ``--out $OUT``.
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------------------------------------------------------------------------------
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_`Run separate commands`
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------------------------------------------------------------------------------
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--ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz \
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--no_surfaces
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------------------------------------------------------------------------------
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_`Run one command`
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------------------------------------------------------------------------------
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The Mindboggle Docker container can be run as a single command to process
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a T1-weighted MR brain image through FreeSurfer, ANTs, and Mindboggle.
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Skip to the next section if you wish to run ``recon-all``,
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``antsCorticalThickness.sh``, and ``mindboggle`` differently::
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docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID
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Outputs are stored in $DOCK/mindboggle123_output/ by default,
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but you can set a different output path with ``--out $OUT``.
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------------------------------------------------------------------------------
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_`Visualize output`
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------------------------------------------------------------------------------

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