diff --git a/Dockerfile b/Dockerfile index fdc10a4..68a9b18 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ FROM pennlinc/atlaspack:0.1.0 as atlaspack -FROM ubuntu:bionic-20220531 +FROM ubuntu:jammy-20240125 # Pre-cache neurodebian key COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg @@ -148,27 +148,10 @@ ENV AFNI_MODELPATH="/usr/lib/afni/models" \ ENV PATH="/usr/lib/afni/bin:$PATH" -# Install FreeSurfer -# Only grab elements we need for ASLPrep -RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz | tar zxv --no-same-owner -C /opt \ - --exclude="freesurfer/diffusion" \ - --exclude="freesurfer/docs" \ - --exclude="freesurfer/fsfast" \ - --exclude="freesurfer/lib/cuda" \ - --exclude="freesurfer/lib/qt" \ - --exclude="freesurfer/matlab" \ - --exclude="freesurfer/mni/share/man" \ - --exclude="freesurfer/subjects/fsaverage_sym" \ - --exclude="freesurfer/subjects/fsaverage3" \ - --exclude="freesurfer/subjects/fsaverage4" \ - --exclude="freesurfer/subjects/cvs_avg35" \ - --exclude="freesurfer/subjects/cvs_avg35_inMNI152" \ - --exclude="freesurfer/subjects/bert" \ - --exclude="freesurfer/subjects/lh.EC_average" \ - --exclude="freesurfer/subjects/rh.EC_average" \ - --exclude="freesurfer/subjects/sample-*.mgz" \ - --exclude="freesurfer/subjects/V1_average" \ - --exclude="freesurfer/trctrain" +# FreeSurfer 7.3.2 +COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt +RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \ + | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt ENV FSF_OUTPUT_FORMAT="nii.gz" \ FREESURFER_HOME="/opt/freesurfer" diff --git a/docker/files/freesurfer7.3.2-exclude.txt b/docker/files/freesurfer7.3.2-exclude.txt new file mode 100644 index 0000000..3b07a64 --- /dev/null +++ b/docker/files/freesurfer7.3.2-exclude.txt @@ -0,0 +1,868 @@ +freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr +freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh +freesurfer/average/711-2B_as_mni_average_305.4dfp.img +freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec +freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.hdr +freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img.rec +freesurfer/average/711-2C_as_mni_average_305.4dfp.hdr +freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec +freesurfer/average/711-2C_as_mni_average_305.4dfp.mat +freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca +freesurfer/average/BrainstemSS +freesurfer/average/Buckner_JNeurophysiol11_MNI152 +freesurfer/average/Choi_JNeurophysiol12_MNI152 +freesurfer/average/colortable_desikan_killiany.txt +freesurfer/average/face.gca +freesurfer/average/HippoSF +freesurfer/average/label_scales.dat +freesurfer/average/lh.atlas2002_simple.gcs +freesurfer/average/lh.atlas2005_simple.gcs 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