Dockerfile_FreeSurfer

FROM freesurfer/freesurfer:7.3.1 AS freesurfer
FROM ubuntu:18.04
ARG TAG_ANTS

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_binarize  \
  /opt/freesurfer/bin/mri_binarize

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_convert  \
  /opt/freesurfer/bin/mri_convert

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_nu_correct.mni  \
  /opt/freesurfer/bin/mri_nu_correct.mni

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_rigid_register \
  /opt/freesurfer/bin/mri_rigid_register

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_robust_register  \
  /opt/freesurfer/bin/mri_robust_register

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mris_calc  \
  /opt/freesurfer/bin/mris_calc

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_segstats  \
  /opt/freesurfer/bin/mri_segstats

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_robust_template \
  /opt/freesurfer/bin/mri_robust_template

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/lta_convert  \
  /opt/freesurfer/bin/lta_convert

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/lta_diff  \
  /opt/freesurfer/bin/lta_diff

COPY --from=freesurfer \
  /usr/local/freesurfer/python/scripts/mri_synthseg  \
  /opt/freesurfer/bin/mri_synthseg

COPY --from=freesurfer \
  /usr/local/freesurfer/models  \
  /opt/freesurfer/models

COPY --from=freesurfer \
  /usr/local/freesurfer/python/scripts/mri_synthstrip  \
  /opt/freesurfer/bin/mri_synthstrip

COPY --from=freesurfer \
  /usr/local/freesurfer/bin/mri_normalize  \
  /opt/freesurfer/bin/mri_normalize

COPY --from=freesurfer \
  /usr/local/freesurfer/mni  \
  /opt/freesurfer/mni

COPY --from=freesurfer \
  /lib64/libcrypt* \
  /opt/freesurfer/lib/

COPY --from=freesurfer \
  /usr/local/freesurfer/sources.csh \
  /opt/freesurfer/sources.csh