Merge pull request #114 from DCAN-Labs/rmCC

Remove chirality correction from postbibsnet
DCAN-Labs · Aug 19, 2024 · ace7a36 · ace7a36
2 parents b7e4e67 + 02e5470
commit ace7a36
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diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,8 @@
 FROM nvcr.io/nvidia/pytorch:21.11-py3
 
 # Manually update the BIBSnet version when building
-ENV BIBSNET_VERSION="3.3.2"
+
+ENV BIBSNET_VERSION="3.3.0"
 
 # Prepare environment
 RUN apt-get update && \
@@ -49,9 +50,11 @@ RUN apt-get update -qq \
     && rm -rf /var/lib/apt/lists/* \
     && echo "Downloading FSL ..." \
     && mkdir -p /opt/fsl-6.0.5.1 \
-    && curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" \
-    | tar -xzpf - fsl-6.0.5.1-centos7_64.tar.gz -O | tar -xzpC /opt/fsl-6.0.5.1 --no-same-owner --strip-components 1
-
+    && wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" \
+    && tar -xzf bibsnet-v3.3.0.tar.gz fsl-6.0.5.1-centos7_64.tar.gz \
+    && tar -xzf fsl-6.0.5.1-centos7_64.tar.gz -C /opt/fsl-6.0.5.1 --no-same-owner --strip-components 1 \
+    && rm bibsnet-v3.3.0.tar.gz fsl-6.0.5.1-centos7_64.tar.gz
+
 ENV FSLDIR="/opt/fsl-6.0.5.1" \
     PATH="/opt/afni-latest:/opt/ants:/opt/fsl-6.0.5.1/bin:$PATH" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
@@ -66,9 +69,13 @@ ENV FSLDIR="/opt/fsl-6.0.5.1" \
 
 # Installing ANTs 2.3.3 (NeuroDocker build)
 # Note: the URL says 2.3.4 but it is actually 2.3.3
-RUN mkdir -p /opt/ants \
-    && curl -sSL --retry 5 "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
-    | tar -xzC /opt/ants --strip-components 1
+# TESTING: installing ANTS from tier2 tar.gz
+RUN echo "Downloading ANTs ..." && \
+    mkdir -p /opt/ants && \
+    wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" && \
+    tar -xzf bibsnet-v3.3.0.tar.gz ants-Linux-centos6_x86_64-v2.3.4.tar.gz && \
+    tar -xzf ants-Linux-centos6_x86_64-v2.3.4.tar.gz -C /opt/ants --no-same-owner --strip-components 1 && \
+    rm bibsnet-v3.3.0.tar.gz ants-Linux-centos6_x86_64-v2.3.4.tar.gz
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users -u 1000 bibsnet
@@ -89,16 +96,28 @@ ENV nnUNet_preprocessed="/opt/nnUNet/nnUNet_raw_data_base/nnUNet_preprocessed" \
     RESULTS_FOLDER="/opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models"
 
 RUN mkdir -p /opt/nnUNet/nnUNet_raw_data_base/ /opt/nnUNet/nnUNet_raw_data_base/nnUNet_preprocessed /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet /home/bibsnet/data
-#COPY trained_models/Task512_BCP_ABCD_Neonates_SynthSegDownsample.zip /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet
-RUN curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.2.tar.gz" | tar -xzpf - Task526_previous_BIBSNet_Production_Model.tar.gz -O | tar -xzpC /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --no-same-owner --strip-components 1 && \
-    curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.2.tar.gz" | tar -xzpf - Task514_BCP_ABCD_Neonates_SynthSeg_T1Only.tar.gz -O | tar -xzpC /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --no-same-owner --strip-components 1 &&\
-    curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.2.tar.gz" | tar -xzpf - Task515_BCP_ABCD_Neonates_SynthSeg_T2Only.tar.gz -O | tar -xzpC /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --no-same-owner --strip-components 1 && \
-    curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.2.tar.gz" | tar -xzpf - Task540_BIBSNet_Production_Model.tar.gz -O | tar -xzpC /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --no-same-owner --strip-components 1
+
+RUN wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" && \
+    tar -xzf bibsnet-v3.3.0.tar.gz Task540_BIBSnet_Production_T1T2_model.tar.gz && \
+    tar -xzf Task540_BIBSnet_Production_T1T2_model.tar.gz -C /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --strip-components 1 && \
+    rm bibsnet-v3.3.0.tar.gz Task540_BIBSnet_Production_T1T2_model.tar.gz
+
+RUN wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" && \
+    tar -xzf bibsnet-v3.3.0.tar.gz Task541_BIBSnet_Production_T1only_model.tar.gz && \
+    tar -xzf Task541_BIBSnet_Production_T1only_model.tar.gz -C /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --strip-components 1 && \
+    rm bibsnet-v3.3.0.tar.gz Task541_BIBSnet_Production_T1only_model.tar.gz
+
+RUN wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" && \
+    tar -xzf bibsnet-v3.3.0.tar.gz Task542_BIBSnet_Production_T2only_model.tar.gz && \
+    tar -xzf Task542_BIBSnet_Production_T2only_model.tar.gz -C /opt/nnUNet/nnUNet_raw_data_base/nnUNet_trained_models/nnUNet --strip-components 1 && \
+    rm bibsnet-v3.3.0.tar.gz Task542_BIBSnet_Production_T2only_model.tar.gz
 
 COPY run.py /home/bibsnet/run.py
 COPY src /home/bibsnet/src
-COPY bin /home/bibsnet/bin
-RUN curl -sSL "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.2.tar.gz" | tar -xzpf - data.tar.gz -O | tar -xzpC /home/bibsnet/data --no-same-owner --strip-components 1
+RUN wget -O bibsnet-v3.3.0.tar.gz "https://s3.msi.umn.edu/bibsnet-data/bibsnet-v3.3.0.tar.gz" && \
+    tar -xzf bibsnet-v3.3.0.tar.gz data.tar.gz && \
+    tar -xzf data.tar.gz -C /home/bibsnet/data --strip-components 1 && \
+    rm bibsnet-v3.3.0.tar.gz data.tar.gz
 
 COPY requirements.txt  /home/bibsnet/requirements.txt
 
@@ -107,6 +126,6 @@ ENV PATH="${PATH}:/home/bibsnet/"
 RUN cp /home/bibsnet/run.py /home/bibsnet/bibsnet
 
 RUN cd /home/bibsnet/ && pip install -r requirements.txt
-RUN cd /home/bibsnet/ && chmod 555 -R run.py bin src bibsnet
+RUN cd /home/bibsnet/ && chmod 555 -R run.py src bibsnet
 
 ENTRYPOINT ["bibsnet"]
diff --git a/bin/LR_mask_registration.sh b/bin/LR_mask_registration.sh
diff --git a/requirements.txt b/requirements.txt
@@ -2,4 +2,4 @@ nibabel==3.2.1
 nipype==1.8.6
 pandas==1.3.5
 scipy==1.10.0
-niworkflows==1.9.0
+niworkflows==1.9.0
diff --git a/src/bibsnet.py b/src/bibsnet.py
@@ -87,7 +87,10 @@ def run_nnUNet_predict(cli_args):
     """
     to_run = [cli_args["nnUNet"], "-i",
                      cli_args["input"], "-o", cli_args["output"], "-t",
-                     str(cli_args["task"]), "-m", cli_args["model"]]
+                     str(cli_args["task"]), "-m", cli_args["model"], 
+                     "--disable_tta"
+                     ]
+
     LOGGER.verbose(f"Now running nnUNet with these parameters: {to_run}")
     process = subprocess.Popen(to_run, stdout=subprocess.PIPE, universal_newlines=True)
     with process.stdout: