diff --git a/docs/installation.rst b/docs/installation.rst
index 1a874433..e07a8b38 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -21,51 +21,57 @@ Docker Container
In order to run qsiprep in a Docker container, Docker must be `installed
`_.
Once Docker is installed, the recommended way to run qsiprep is to use the
-``qsiprep-docker`` wrapper, which requires Python and an Internet connection.
+``qsiprep-docker`` wrapper, which requires Python and an Internet connection
+and that you install the ``qsiprep-container`` package with ``pip``.
-.. note:: If running Docker Desktop on MacOS, be sure to set the memory to 6 or more GB.
- Too little memory assigned to Docker Desktop can result in a message like ``Killed.``
+.. note:: If running Docker Desktop on MacOS (or via Docker Desktop), be sure to set
+ the memory to 6 or more GB. Too little memory assigned to Docker Desktop can result
+ in a message like ``Killed.``
When run, ``qsiprep-docker`` will generate a Docker command line for you,
print it out for reporting purposes, and then run the command, e.g.::
$ qsiprep-docker /path/to/data/dir /path/to/output/dir participant
- RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
- -v /path/to_output/dir:/out pennbbl/qsiprep:1.0.0 \
+ RUNNING: docker run --rm -it -v /path/to/data/dir:/data \
+ -v /path/to_output/dir:/out pennbbl/qsiprep:latest \
/data /out participant
...
You may also invoke ``docker`` directly::
$ docker run -ti --rm \
- -v filepath/to/data/dir:/data:ro \
- -v filepath/to/output/dir:/out \
+ -v /filepath/to/data/dir \
+ -v /filepath/to/output/dir \
+ -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
pennbbl/qsiprep:latest \
- /data /out participant
+ /filepath/to/data/dir /filepath/to/output/dir participant \
+ --fs-license-file /opt/freesurfer/license.txt
For example: ::
$ docker run -ti --rm \
- -v $HOME/fullds005:/data:ro \
- -v $HOME/dockerout:/out \
+ -v $HOME/fullds005 \
+ -v $HOME/dockerout \
+ -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
pennbbl/qsiprep:latest \
- /data /out participant \
- --ignore fieldmaps
+ $HOME/fullds005 $HOME/dockerout participant \
+ --ignore fieldmaps \
+ --fs-license-file /opt/freesurfer/license.txt
-If you are running Freesurfer as part of QSIPrep,
+If you are running Freesurfer as part of QSIPrep,
you will need to mount your Freesurfer license.txt file when invoking ``docker`` ::
$ docker run -ti --rm \
- -v $HOME/fullds005:/data:ro \
- -v $HOME/dockerout:/out \
+ -v $HOME/fullds005 \
+ -v $HOME/dockerout \
-v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
pennbbl/qsiprep:latest \
- /data /out participant \
+ $HOME/fullds005 -v $HOME/dockerout participant \
--fs-license-file /opt/freesurfer/license.txt
-See `External Dependencies`_ for more information (e.g., specific versions) on
-what is included in the latest Docker images.
+See `External Dependencies`_ for more information on what is included in the Docker image
+and how it's built.
@@ -77,28 +83,22 @@ The easiest way to get a Sigularity image is to run::
$ singularity build qsiprep-.sif docker://pennbbl/qsiprep:
Where ```` should be replaced with the desired version of qsiprep that you want to download.
-Do not use ``latest``.
+Do not use ``latest`` or ``unstable`` unless you are performing limited testing.
As with Docker, you will need to bind the Freesurfer license.txt when running Singularity ::
- $ singularity run --cleanenv \
- -B $HOME/fullds005:/data:ro,$HOME/dockerout:/out,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
+ $ singularity run --containall --writable-tmpfs \
+ -B $HOME/fullds005,$HOME/dockerout,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
qsiprep-.sif \
- /data /out participant \
+ $HOME/fullds005 $HOME/dockerout participant \
--fs-license-file /opt/freesurfer/license.txt
External Dependencies
---------------------
-qsiprep is written using Python 3.6 (or above), and is based on
-nipype_.
-
-qsiprep requires some other non-python neuroimaging software tools:
-
-- ANTs_ (version 2.3.9)
-- AFNI_ (version Debian-16.2.07)
-- FreeSurfer_ (6.0.1)
-- FSL_ (6.0.3)
-- `DSI Studio`_
-- MRtrix_
+qsiprep is written using Python 3.8 (or above), and is based on
+nipype_. The external dependencies are built in the `qsiprep_build
+`_ repository. There
+you can find the URLs used to download the dependency source code
+and the steps to compile each dependency.