Pull request for the MDT docker with charmed model implementation

MDT/Dockerfile

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+FROM ubuntu:16.04
+
+RUN mkdir -p /src
+COPY silent.cfg /src
+
+# install dependencies 
+RUN apt-get update && apt-get install -y lsb-core wget
+
+# install Intel OpenCL runtime
+RUN cd /src && \ 
+    wget http://registrationcenter-download.intel.com/akdlm/irc_nas/9019/opencl_runtime_16.1.1_x64_ubuntu_6.4.0.25.tgz && \
+	tar -xvzf opencl_runtime_16.1.1_x64_ubuntu_6.4.0.25.tgz && \
+	mv silent.cfg opencl_runtime_16.1.1_x64_ubuntu_6.4.0.25 && \
+	cd opencl_runtime_16.1.1_x64_ubuntu_6.4.0.25 && \
+	./install.sh --silent silent.cfg --cli-mode
+
+# install mdt
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && apt-get install -y software-properties-common && add-apt-repository ppa:robbert-harms/cbclab
+RUN apt-get update && apt-get install -y python3-mdt python3-pip
+RUN pip3 install tatsu==4.2.6
+
+
+# Copy the source files (only this layer will have to be built after the first time)
+COPY mdt_script.py /scripts/
+
+
+ENTRYPOINT ["/usr/bin/python3", "/scripts/mdt_script.py"] 

MDT/mdt_script.py

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+"""
+Simple script that runs CHARMED model from MDT.
+
+
+"""
+
+import numpy as np
+import nibabel as nib
+import sys
+
+import mdt
+
+
+def doCHARMED(input_data_filename, bval_filename, bvec_filename, mask_data_filename,TE):
+    protocol = mdt.create_protocol(
+        bvecs=bvec_filename, bvals=bval_filename,
+        out_file='/data/mdt.prtcl',
+        TE=TE)
+
+    input_data = mdt.load_input_data(
+        input_data_filename,
+        '/data/mdt.prtcl',
+        mask_data_filename)
+
+    mdt.fit_model('CHARMED_r1', input_data, '/data/charmed_')
+
+if __name__ == '__main__':
+    data_path = '/data/'
+    #data_path = '/home/ricardo/brainhack-variations'
+
+    input_data_filename = data_path + str(sys.argv[1])
+    bval_filename = data_path + str(sys.argv[2])
+    bvec_filename = data_path + str(sys.argv[3])
+    mask_data_filename = data_path + str(sys.argv[4])
+    TE = float(sys.argv[5])
+
+    doCHARMED(input_data_filename, bval_filename, bvec_filename,  mask_data_filename, TE)

MDT/silent.cfg

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+# Patterns used to check silent configuration file
+#
+# anythingpat - any string
+# filepat     - the file location pattern (/file/location/to/license.lic)
+# lspat       - the license server address pattern (0123@hostname)
+# snpat       - the serial number pattern (ABCD-01234567)
+
+# accept EULA, valid values are: {accept, decline}
+ACCEPT_EULA=accept
+
+# install mode for RPM system, valid values are: {RPM, NONRPM}
+INSTALL_MODE=NONRPM
+
+# optional error behavior, valid values are: {yes, no}
+CONTINUE_WITH_OPTIONAL_ERROR=yes
+
+# install location, valid values are: {/opt, filepat}
+PSET_INSTALL_DIR=/opt
+
+# continue with overwrite of existing installation directory, valid values are: {yes, no}
+CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
+
+# list of components to install, valid values are: {ALL, DEFAULTS, anythingpat}
+COMPONENTS=DEFAULTS
+
+# installation mode, valid values are: {install, modify, repair, uninstall}
+PSET_MODE=install
+
+# directory for non-RPM database, valid values are: {filepat}
+#NONRPM_DB_DIR=filepat
+
+# Intel(R) Software Improvement Program opt-in, valid values are: {yes, no}
+PHONEHOME_SEND_USAGE_DATA=no
+
+# Perform validation of digital signatures of RPM files, valid values are: {yes, no}
+SIGNING_ENABLED=yes
+