BART on the scanner.

bartfire.py

@@ -12,6 +12,11 @@
 # Folder for debug output files
 debugFolder = "/tmp/share/debug"
 
+# Don't write to /tmp/share in cfl
+os.environ["TMPDIR"] = "/tmp"
+
+use_nlinv = False
+
 def process(connection, config, metadata):
     logging.info("Config: \n%s", config)
 
@@ -45,7 +50,7 @@ def process(connection, config, metadata):
             if isinstance(item, ismrmrd.Acquisition):
                 # Accumulate all imaging readouts in a group
                 if (not item.is_flag_set(ismrmrd.ACQ_IS_NOISE_MEASUREMENT) and
-                    not item.is_flag_set(ismrmrd.ACQ_IS_PARALLEL_CALIBRATION) and
+                    (use_nlinv or not item.is_flag_set(ismrmrd.ACQ_IS_PARALLEL_CALIBRATION)) and
                     not item.is_flag_set(ismrmrd.ACQ_IS_PHASECORR_DATA)):
                     acqGroup.append(item)
 
@@ -131,19 +136,26 @@ def process_raw(group, config, metadata):
     logging.debug("Raw data is size %s" % (data.shape,))
     np.save(debugFolder + "/" + "raw.npy", data)
 
-    # Fourier Transform with BART
-    logging.info("Calling BART FFT")
-    data = bart(1, 'fft -u -i 3', data)
+    # Reconstruction with BART.
+    if use_nlinv:
+        logging.info("Calling BART NLINV")
+
+        # coil compression to 8 channels
+        data = bart(1, "cc -p8", data)
+
+        # nlinv with debug level 4 and 13 gauss-newton steps.
+        data = bart(1, "nlinv -d4 -i13", data)
+
+        data = np.atleast_3d(abs(data))
+
+    else:
+        logging.info("Calling BART FFT")
+        data = bart(1, 'fft -u -i 3', data)
 
-    # Re-format as [cha row col phs]
-    data = data.transpose((3, 0, 1, 2))
+        # RSS with BART
+        data = bart(1, 'rss 8', data)
 
-    # Sum of squares coil combination
-    # Data will be [PE RO phs]
-    data = np.abs(data)
-    data = np.square(data)
-    data = np.sum(data, axis=0)
-    data = np.sqrt(data)
+        data = np.atleast_3d(data.real)
 
     logging.debug("Image data is size %s" % (data.shape,))
     np.save(debugFolder + "/" + "img.npy", data)

docker/bart/Dockerfile

@@ -1,5 +1,5 @@
 # ----- First stage to build BART -----
-FROM python:3.9-slim AS bart_build
+FROM python:3.12.0-slim AS bart_build
 ARG  DEBIAN_FRONTEND=noninteractive
 ENV  TZ=America/Chicago
 
@@ -8,19 +8,24 @@ RUN  mkdir -p /opt/code
 
 # BART (static linked)
 RUN cd /opt/code                                   && \
-    git clone https://github.com/mrirecon/bart.git --branch v0.7.00 && \
+    git clone https://github.com/mrirecon/bart.git --branch v0.9.00 && \
     cd bart                                        && \
-    make SLINK=1 -j $(nproc)                       && \
+    make -j $(nproc)                               && \
     make install
 
 # ----- Main stage without build dependencies -----
 # Re-use already built Docker image, but the contents of \docker\Dockerfile can also be
 # recapitulated here instead to ensure the latest build
 FROM kspacekelvin/fire-python
+
+# this does *not* work in the chroot image!
 ENV PYTHONPATH=/opt/code/bart/python
 
 # Copy BART from previous stage
 COPY --from=bart_build /usr/local/bin/bart             /usr/local/bin/
 COPY --from=bart_build /usr/local/lib/bart/commands    /usr/local/lib/bart/commands
 COPY --from=bart_build /usr/local/share/doc/bart       /usr/local/share/doc/bart
 COPY --from=bart_build /opt/code/bart                  /opt/code/bart
+
+# Install BART runtime dependencies
+RUN  apt-get update && apt-get install -y libfftw3-single3 libgomp1 liblapacke libpng16-16 libblas3 libunwind8

docker/docker_tar_to_chroot.sh

@@ -2,6 +2,8 @@
 # This script takes a Docker container export (.tar) creates a chroot image (.img)
 # Note that root privileges are required to mount the loopback images 
 
+set -eu
+
 # Syntax: ./docker_tar_to_chroot.sh docker-export.tar chroot.img
 
 EXPORT_FILE=${1}
@@ -40,6 +42,7 @@ tar -xf ${EXPORT_FILE} --directory=/mnt/chroot --totals
 df -h
 
 umount /mnt/chroot
+rmdir /mnt/chroot
 
 echo Finished!  Verify that no errors have occured and that available space on the 
 echo last row of the above df output is greater than 100 MB

start-fire-python-server.sh

@@ -9,6 +9,10 @@
 # it's less likely to accidentally fill up the chroot
 export TMPDIR=/tmp/share
 
+# This is needed for the chroot-images to run BART.
+export PYTHONPATH=/opt/code/bart/python:${PYTHONPATH}
+
+
 if [ $# -eq 1 ]; then
   LOG_FILE=${1}
   python3 /opt/code/python-ismrmrd-server/main.py -v -r -H=0.0.0.0 -p=9002 -l=${LOG_FILE} &