@@ -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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+
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+ docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID
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+
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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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------------------------------------------------------------------------------
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_`Run separate commands `
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------------------------------------------------------------------------------
@@ -209,19 +222,6 @@ Generate only volume (no surface) labels and shapes::
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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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-
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- docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle mindboggle123 $IMAGE --id $ID
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-
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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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------------------------------------------------------------------------------
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_`Visualize output `
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------------------------------------------------------------------------------
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