From c5ee3948674cead15c9b4f28f07c7ce01fa1fc8e Mon Sep 17 00:00:00 2001 From: Dan Levitas Date: Tue, 27 Aug 2024 15:54:11 +0000 Subject: [PATCH] [ENH] Enable fslreorient2std during defacing --- handler/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/handler/Dockerfile b/handler/Dockerfile index f86d043..b78c804 100755 --- a/handler/Dockerfile +++ b/handler/Dockerfile @@ -7,7 +7,7 @@ ENV DEBIAN_FRONTEND noninteractive RUN apt update && \ apt-get update && apt-get upgrade -y -RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy +RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy bc RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \ pip3 install quickshear mne mne-bids @@ -30,7 +30,9 @@ RUN echo "DEFAULT_METADATA_JSON=/usr/local/lib/python3.8/dist-packages/pypet2bid RUN mkdir -p /usr/local/fsl && \ git clone https://github.com/dlevitas/FSL_binaries /usr/local/fsl && \ - rm -rf /usr/local/fsl/README.md + rm -rf /usr/local/fsl/README.md && \ + mkdir -p /usr/local/fsl/data/standard && \ + mv /usr/local/fsl/bin/MNI152_T1_2mm_brain.nii.gz /usr/local/fsl/data/standard ENV FSLDIR=/usr/local/fsl ENV PATH=$PATH:$FSLDIR/bin