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20200507-fs7-neurodocker.md

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Docker Containers for FreeSurfer 7

FreeSurfer 7 docker containers. Created using neurodocker. Big thanks to @kaczmarj and @satra for their guidance and for making such an amazing tool!

This documents how the following containers were created using this fork of neurodocker.

  • pwighton/freesurfer:7.0.0 (6.21GB)
    • Installs FS7 tarball. Most of FS7 should work, but Matlab MCR is not in the container.
  • pwighton/freesurfer:7.0.0-mcr (7.76GB)
    • Installs FS7 tarball and Matlab MCR 2014b
  • pwighton/freesurfer:7.0.0-min (1.33GB)
    • Installs FS7, but then removes every file from the container that is not used during recon-all
  • pwighton/freesurfer:7.0.0-min-mcr (2.93GB)
    • Installs FS7, but then removes every file from the container that is not used during
      • recon-all
      • segmentBS.sh
      • segmentHA_T2.sh

freesurfer:7.0.0

neurodocker generate docker \
  --base continuumio/miniconda:4.7.12 \
  --pkg-manager apt \
  --freesurfer version=7.0.0 \
    | docker build -t pwighton/freesurfer:7.0.0 -

freesurfer:7.0.0-mcr

neurodocker generate docker \
  --base continuumio/miniconda:4.7.12 \
  --pkg-manager apt \
  --freesurfer version=7.0.0 \
  --matlabmcr version=2014b install_path=/opt/MCRv84 \
  --run "ln -s /opt/MCRv84/v84 /opt/freesurfer-7.0.0/MCRv84" \
    | docker build -t pwighton/freesurfer:7.0.0-mcr -

freesurfer:7.0.0-min

Grab ref data:

rsync -aL psydata.ovgu.de::studyforrest/structural/sub-01 \
  /home/paul/cmet/data/studyforrest-data-structural

Create a subjects dir:

mkdir -p /tmp/fs-subs

Generate the freesurfer:7.0.0 container, then invoke it:

docker run --rm -it --security-opt seccomp:unconfined \
  -v /home/paul/cmet/data/studyforrest-data-structural:/data \
  -v /tmp/fs-subs:/fsdata \
  -v /home/paul/cmet/license.txt:/license.txt \
  -e FS_LICENSE='/license.txt' \
  -e SUBJECTS_DIR='/fsdata' \
  --name fs7 \
  pwighton/freesurfer:7.0.0 \
    /bin/bash

In another terminal, trace the following commands:

cmd1="recon-all -s sub-01 -all -i /data/sub-01/anat/sub-01_T1w.nii.gz -T2 /data/sub-01/anat/sub-01_T2w.nii.gz -T2pial"
cmd2="asegstats2table --subjects sub-01 --segno 11 17 18 --meas mean --tablefile aseg.mean-intensity.table"
cmd3="aparcstats2table --hemi lh --subjects sub-01 --tablefile lh.aparc.area.table"

With neurodocker-minify

neurodocker-minify --container fs7 \
  --dirs-to-prune /opt/freesurfer-7.0.0 \
  --commands "$cmd1" "$cmd2" "$cmd3"

Enter 'y' when prompted and tag resulting container as freesurfer:7.0.0-min

freesurfer:7.0.0-min-mcr

Grab ref data:

rsync -aL psydata.ovgu.de::studyforrest/structural/sub-01 \
  /home/paul/cmet/data/studyforrest-data-structural

Create a subjects dir:

mkdir -p /tmp/fs-subs

Generate the freesurfer:7.0.0-mcr container, then invoke it:

docker run --rm -it --security-opt seccomp:unconfined \
  -v /home/paul/cmet/data/studyforrest-data-structural:/data \
  -v /tmp/fs-subs:/fsdata \
  -v /home/paul/cmet/license.txt:/license.txt \
  -e FS_LICENSE='/license.txt' \
  -e SUBJECTS_DIR='/fsdata' \
  --name fs7 \
  pwighton/freesurfer:7.0.0-mcr \
    /bin/bash

In another terminal, trace the following commands:

cmd1="recon-all -s sub-01 -all -i /data/sub-01/anat/sub-01_T1w.nii.gz -T2 /data/sub-01/anat/sub-01_T2w.nii.gz -T2pial"
cmd2="segmentBS.sh sub-01"
cmd3="segmentHA_T2.sh sub-01 /data/sub-01/anat/sub-01_T2w.nii.gz t2 1"
cmd4="asegstats2table --subjects sub-01 --segno 11 17 18 --meas mean --tablefile aseg.mean-intensity.table"
cmd5="aparcstats2table --hemi lh --subjects sub-01 --tablefile lh.aparc.area.table"

With neurodocker-minify:

neurodocker-minify --container fs7 \
  --dirs-to-prune /opt/freesurfer-7.0.0 \
  --commands "$cmd1" "$cmd2" "$cmd3" "$cmd4" "$cmd5"

Enter 'y' when prompted and tag resulting container as freesurfer:7.0.0-min-mcr